Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Thanks. But when I ran make again I am getting this error [ 0%] Built target gmxfftw make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 shahid Nayeem On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote: For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have this problem. Run make a second time and it will work. Mark On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com wrote: Thanks Wahab I followed your instruction and added #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h. Then again in make command I got following errors. [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to compile gromacs 4.6.3 on cygwin Shahid Nayeem On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. ... /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/** impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target The Gromacs-file gmxlib/thread_mpi/impl.h is missing the correct #define for the unixish Cygwin pseudo-os. You can add it by inserting #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h Then the package will probably compile and link, but mdrun's thread-mpi (tMPI) will not work on Cygwin (didn't work last time I tried). So you could do the following: 1) install the Gromacs package with normal compilation, and 2) build and install the openmpi-version of mdrun (mdrun_mpi). (1) cmake-options for package: ... -DGMX_GPU=OFF
Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Thanks Mark $ make [ 0%] Built target gmxfftw make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 I checked in folder /cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a , this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to locate it. Please help me shahid Nayeem On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem msnay...@gmail.com wrote: Thanks. But when I ran make again I am getting this error [ 0%] Built target gmxfftw make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 shahid Nayeem On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote: For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have this problem. Run make a second time and it will work. Mark On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com wrote: Thanks Wahab I followed your instruction and added #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h. Then again in make command I got following errors. [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to compile gromacs 4.6.3 on cygwin Shahid Nayeem On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. ... /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/** impl.h:504:20: error: field ‘timer_init’ has incomplete type
[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o In file included from /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to install this version of gromacs on cygwin Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
Thanks Wahab I followed your instruction and added #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h. Then again in make command I got following errors. [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o [ 53%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o [ 55%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a', needed by `src/gmxlib/cyggmx_d-8.dll'. Stop. CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to compile gromacs 4.6.3 on cygwin Shahid Nayeem On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. ... /cygdrive/c/packages/gromacs-**4.6.3/src/gmxlib/thread_mpi/** impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/**build.make:3070: recipe for target The Gromacs-file gmxlib/thread_mpi/impl.h is missing the correct #define for the unixish Cygwin pseudo-os. You can add it by inserting #define HAVE_SYS_TIME_H at the very top of the file gmxlib/thread_mpi/impl.h Then the package will probably compile and link, but mdrun's thread-mpi (tMPI) will not work on Cygwin (didn't work last time I tried). So you could do the following: 1) install the Gromacs package with normal compilation, and 2) build and install the openmpi-version of mdrun (mdrun_mpi). (1) cmake-options for package: ... -DGMX_GPU=OFF \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install (delete all files from the build path) (2) cmake options for mdrun_mpi ... -DGMX_GPU=OFF\ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON \ ... make -j4 install-mdrun The openmpi-version (mdrun_mpi) runs reasonable on Cygwin/64 1.7.25, but not as fast as the native windows version (compiled with visual studio 10 or 12). The windows-compiled version of 4.6.3 is very robust and allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12) for unknown reasons). Then, you'll have full gpu support under windows. Regards M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp
[gmx-users] installing Gromacs4.6.3 on cygwin
Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_permute.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_position.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_same.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/sm_simple.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/selection/symrec.c.o [ 15%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/indexutil.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/poscalc.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/gmx_statistics.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/statistics/histogram.c.o [ 16%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o In file included from /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: error: field ‘timer_init’ has incomplete type struct timeval timer_init; ^ src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 Please help me to install this version of gromacs on cygwin Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
It is a peptide. Shahid On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen jesoren...@ucsd.edu wrote: Shahid, This must be system dependent then because there are experimental methods, e.g. NMR and CD, that can help determine the secondary structure of proteins/peptides are various pH ranges. What is your system? A peptide? A globular protein? Best, Jesper On May 3, 2013, at 7:33 PM, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH environment of the cell. Experimentally it is not known but it has been proposed by many that the change in pH leads to change in conformation. I did constant protonation state MD at two different pH. I got an alpha helix converting to beta sheet at higher pH but not at lower pH. I am bothered to prove the reliability of the simulation results as experimentally it cant be established. Shahid On Sat, May 4, 2013 at 5:46 AM, bapti...@itqb.unl.pt wrote: Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are methods to perform what is called constant-pH MD, where the protonation states of those groups change in a discrete or continuous way along the simulation. If you are interested, start with the corresponding GROMACS how-to ( http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and then search the literature. In any case, you don't need any of that fancy stuff unless you have reasons to think that the properties you want to study in your system are strongly dependent on protonation-conformation coupling effects. In some cases you may be suspicious about the effect of the protonation state of one group (e.g., a histidine), but that can be simply tested by performing two constant-protonation MD simulations, one for each state (you can even try to use a linear response approximation on top of that). But in most cases you don't need even that. For what it's worth: I was one of the first to develop and apply constant-pH MD and I don't bother to use it most of the time... :) Best, Antonio On Fri, 3 May 2013, Erik Marklund wrote: Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please
Re: [gmx-users] constant protonation state MD
Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH environment of the cell. Experimentally it is not known but it has been proposed by many that the change in pH leads to change in conformation. I did constant protonation state MD at two different pH. I got an alpha helix converting to beta sheet at higher pH but not at lower pH. I am bothered to prove the reliability of the simulation results as experimentally it cant be established. Shahid On Sat, May 4, 2013 at 5:46 AM, bapti...@itqb.unl.pt wrote: Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are methods to perform what is called constant-pH MD, where the protonation states of those groups change in a discrete or continuous way along the simulation. If you are interested, start with the corresponding GROMACS how-to ( http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulationhttp://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and then search the literature. In any case, you don't need any of that fancy stuff unless you have reasons to think that the properties you want to study in your system are strongly dependent on protonation-conformation coupling effects. In some cases you may be suspicious about the effect of the protonation state of one group (e.g., a histidine), but that can be simply tested by performing two constant-protonation MD simulations, one for each state (you can even try to use a linear response approximation on top of that). But in most cases you don't need even that. For what it's worth: I was one of the first to develop and apply constant-pH MD and I don't bother to use it most of the time... :) Best, Antonio On Fri, 3 May 2013, Erik Marklund wrote: Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http
[gmx-users] constant protonation state MD
Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send
[gmx-users] topology
Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file. shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx. shahid On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 10:39 AM, shahid nayeem wrote: Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file. You may be able to use the -cys option to fool pdb2gmx, but I don't know if that will cause problems. Having half a disulfide present is odd, though some force fields support thiolate or neutral (i.e. radical) forms of cysteine. You'll have to look into the force field files to see what's available. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] boundwaters
Hi Justin If I use the boundwaters.ndx to write another .ndx file using 1 2 3 4 and so on over all snapshots then also I should get the common water molecules in these snapshots. Am I right. Shahid On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/28/13 10:02 AM, shahid nayeem wrote: Dear Users I am interested in knowing only the water molecules which remains bounded to the protein during MD. Using g_select I can make a boundwater.ndx file which gives water molecules within a specified distance from the protein but it gives different water molecule from each snapshot. Now I want onle those water which is common in all frames. How to proceed from here and is there any other way to do this. Please help. You should be able to write a simple script that runs through each group, stores the atom numbers, and then checks which ones are common to all frames. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] building_insertion_mutants
Dear all I am repeating this mail as it could not get uploaded on site. Please suggest me that whether I can insert 15 residue sequence in an existing pdb file and can I get the minimized altered coordinates from here. If not then please suggest an external software or server where I can model this protein and get the pdb of protein with inserted peptide segment. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generating insertion mutants
Dear all Please suggest me a tool with which I can generate insertion mutants from a .pdb file. I want to insert new 10-15 aa sequence of AA in between an existing .pdb file. The tool should write a new .pdb file with altered coordinates after insertion of new sequence and minimization of the structure. shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] LINCS
Dear all One basic clarification. How does LINCS algorithm influences the results of final production run. In what respect a minimization, pr and final simulation done with constraints = none and with constraint= all_bonds are different. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS
Right, I have a pdb where some of the residues are missing and when I try to simulate it I get LINCS warning in between the atom of the two ends of missing residues. So if I use a smaller time step (0.01) for final production run and energy minimization with setting constraint = none, making it computationally more expensive. Will these results will be O.K. Shahid Nayeem On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 2:02 PM, shahid nayeem wrote: Dear all One basic clarification. How does LINCS algorithm influences the results of final production run. In what respect a minimization, pr and final simulation done with constraints = none and with constraint= all_bonds are different. Sounds like you should do some background reading on how and why constraints work. Manual and refs therein are good starting points. Or your favourite molecular simulation textbook. In a nutshell, you use them in production simulation because they're a reasonable model and allow a larger time step. You might avoid them when you're not yet at equilbrium, because their implementation can be brittle when your structure doesn't agree with the model physics. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS
I want to simulate without building the missing residue. Does gromacs have an option of capping. I am using Gromacs 4.5.4. If not then suggest some software which I may use. Shahid nayeem On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 2:28 PM, shahid nayeem wrote: Right, I have a pdb where some of the residues are missing and when I try to simulate it I get LINCS warning in between the atom of the two ends of missing residues. So if I use a smaller time step (0.01) for final production run and energy minimization with setting constraint = none, making it computationally more expensive. Will these results will be O.K. Does it sound OK to model missing residues with solvent (or vacuum) and have a chemical bond between the dangling ends? It's also definitely not OK to ignore the warning pdb2gmx gave you about this bond being too long. Plowing ahead blindly costs more time than than being careful and painstaking. You need to either cap your chains or build in the missing residues with non-GROMACS software, but what's best depends what you're trying to observe. Mark Shahid Nayeem On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 2:02 PM, shahid nayeem wrote: Dear all One basic clarification. How does LINCS algorithm influences the results of final production run. In what respect a minimization, pr and final simulation done with constraints = none and with constraint= all_bonds are different. Sounds like you should do some background reading on how and why constraints work. Manual and refs therein are good starting points. Or your favourite molecular simulation textbook. In a nutshell, you use them in production simulation because they're a reasonable model and allow a larger time step. You might avoid them when you're not yet at equilbrium, because their implementation can be brittle when your structure doesn't agree with the model physics. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generating_tpr_file from.xtc
Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
I have added some new windows in mutant umbrella sampling which removes the sampling gap around 4 nm. Also I sampled more windows in the initial COM distance in the hope that I get energy minimum of profile well defined. I also did boot strapping for error estimates. The files can be assessed at http://www.freefilehosting.net/umbrellamut On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: The attached profile.xvg and histo.xvg are here. sorry for sending earlier mail without attachments Shahid Nayeem On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem msnay...@gmail.commailto: msnay...@gmail.com wrote: As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. I wouldn't base any conclusions off of them. You have a sampling gap at just over 4 nm in the mutant simulations. More importantly, you do not have a defined energy minimum in the mutant windows so it is impossible to calculate a reliable value for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it. -Justin Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] Umbrella_pull_simulation
The similar files for wt can be assesed at http://www.freefilehosting.net/umbrellawt I expected wild type binding energy to be less than mutant The command used for g_wham is g_wham_mpi_4.5.4 -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg -hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac I get the values exactly opposite to my expectation and unable to find out where I am wrong please suggest. Shahid Nayeem On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem msnay...@gmail.com wrote: I have added some new windows in mutant umbrella sampling which removes the sampling gap around 4 nm. Also I sampled more windows in the initial COM distance in the hope that I get energy minimum of profile well defined. I also did boot strapping for error estimates. The files can be assessed at http://www.freefilehosting.net/umbrellamut On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: The attached profile.xvg and histo.xvg are here. sorry for sending earlier mail without attachments Shahid Nayeem On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem msnay...@gmail.commailto: msnay...@gmail.com wrote: As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. I wouldn't base any conclusions off of them. You have a sampling gap at just over 4 nm in the mutant simulations. More importantly, you do not have a defined energy minimum in the mutant windows so it is impossible to calculate a reliable value for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it. -Justin Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org
Re: [gmx-users] Umbrella_pull_simulation
As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement. Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code). -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. Shahid Nayeem On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My protein complex interface has a hydrophobic core and on each side of this core at the edge are two hydrogen bonds. The Hydrogen bond on one side is between Arg and Asp and another side it is between Arg and Glu. Its experimental Kd is in nanomolar regions. How should I decide the length of the simulation required in each window with this information. As you would any other system. Look for convergence of observables of interest. Your PMF alone suggests insufficient sampling for these simulations, so as I've said several times, you probably need longer simulations to do so, but you can start by examining the physical properties of each window. What you're looking for is up to you, based on your knowledge of the system at hand. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
My system is a protein-protein complex. After pulling I selected windows at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter windows at 0.2nm spacing was selected upto 7.5nm. In each window 10ns MD was done and g_wham command was run neglecting the fist 1ns run for equilibriation. Shahid Nayeem On Tue, Feb 21, 2012 at 6:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it. I don't know. You've never even stated what your system is, how you decided on the window spacing or time in each window, etc. It may be that your simulations are too short. You have a few regions along the reaction coordinate that are not well-sampled, which could contribute to some rockiness in the PMF. -Justin Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim = YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. They're not terrible, but could be better. The PMF profile is a little rough and there are some regions of the reaction coordinate with little sampling. Maybe your simulations need to be longer and/or you need to exclude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering). -Justin Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp
Re: [gmx-users] Umbrella_pull_simulation
I thought this time to be sufficient without any reasonable basis. shahid Nayeem On Fri, Feb 24, 2012 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My system is a protein-protein complex. After pulling I selected windows at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter windows at 0.2nm spacing was selected upto 7.5nm. In each window 10ns MD was done and g_wham command was run neglecting the fist 1ns run for equilibriation. OK, so how did you decide that 10 ns was sufficient in each window? -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
My protein complex interface has a hydrophobic core and on each side of this core at the edge are two hydrogen bonds. The Hydrogen bond on one side is between Arg and Asp and another side it is between Arg and Glu. Its experimental Kd is in nanomolar regions. How should I decide the length of the simulation required in each window with this information. Shahid nayeem On Fri, Feb 24, 2012 at 7:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I thought this time to be sufficient without any reasonable basis. If you pick an arbitrary time frame, you're going to get results with arbitrary accuracy. Your time frame should be decided based on a whole host of factors, not the least of which include an assessment of the types of interactions in the system and how they may decay as a function of distance, as well as the individual convergence of observables in each simulation. This is true of any simulation. Only after you can conclude that each window has converged can you expect to draw any reasonable conclusions. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. Shahid Nayeem On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem msnay...@gmail.com wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists profile.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it. Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. They're not terrible, but could be better. The PMF profile is a little rough and there are some regions of the reaction coordinate with little sampling. Maybe your simulations need to be longer and/or you need to exclude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering). -Justin Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists profile.xvg Description
Re: [gmx-users] Umbrella_pull_simulation
Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. shahid Nayeem On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am doing umbrella sampling for a protein complex. After analysis I am finding that prifle.xvg has not converged. Now I want to extend simulation. I have already pulled one chain to the length of the box. Can I further pull by extending the box size and add more windows to umbrella sampling. Please suggest. You would have to use a simple test system to prove that this is a valid approach. Changing the nature of the system for some windows sounds very questionable to me, and likely would be to reviewers. How one should ascertain the initial box size so that g_wham gives a converged profile.xvg. You should determine the distance needed to sufficiently separate your components, that is, determine the minimum COM distance at which interaction between the two species is negligible. Ideally, they would be non-interacting, but with PME, that is not possible. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella_pull_simulation
Dear All I am doing umbrella sampling for a protein complex. After analysis I am finding that prifle.xvg has not converged. Now I want to extend simulation. I have already pulled one chain to the length of the box. Can I further pull by extending the box size and add more windows to umbrella sampling. Please suggest. How one should ascertain the initial box size so that g_wham gives a converged profile.xvg. Please help. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella_pulling_simulation
Dear All How does the terminal group capping/ionization state will influence the Free energy obtained from g_wham in umbrella sampling simulation. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Number of windows in umbrella sampling
Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and doing umbrella sampling. In the end when you see histo.xvg and profile.xvg , it cost a lot computationally and if you don't get it right these computational resources are wasted. Shahid nayeem On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks for quick reply. I have created mutant of a complex by changing interface residue in VMD. These mutant are experimentally known to show less binding affinity. I want to reproduce these results with umbrella sampling. Now I am sending profile and histo file for wt and mutant. Please suggest where i am wrong. The PMF curves look poorly converged. Your reaction coordinates are not the same for both the WT and mutant (you appear to have a far shorter reaction coordinate for the mutant). The energy minimum is also ill-defined for the mutant. As for the reason behind these phenomena, I cannot say, nor do I have time to sort through your data and try to work it out for you. Refer to the literature, find similar protocols, and proceed from there. -Justin Shahid Nayeem On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: Dear Justin I am doing umbrella pulling simulation of a protein complex wt and mutant. I expect mutant to give lower deltG value. I am attaching a tif file of energy vs time curve of wt and mutant protein on pulling simulation. These energies are obtained by g_energy and selecting 11 option which is COM pulling energy. In this curve the first peak decreases and again rises at longer time. How many windows should be selected. As expected the peak of COM pulling energy is lower in mutants. Please explain why the energy again rises at higher time. Should I use the windows upto 160ps only because thereafter in both curve there is rise in energy value. the pull code used is as follows. What you have obtained is a path-dependent energy that may or may not signify anything useful - it almost certainly does not. I cannot offer an explanation of the sharp increase towards the end of the simulation other than to speculate that your box is of insufficient size and you're encountering PBC issues. As for how many windows are necessary, it's also impossible to tell. You need enough windows to adequately sample the reaction coordinate. Thus, it is decided based on how far you need to separate the two species, how strong the force constant is during the US simulations, the nature of the interactions in the system and how fast they converge, etc. -Justin pull_geometry = distance pull_dim= Y N Y pull_vec1 = 0.75 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 pull_k1 = 1000 -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
Re: [gmx-users] Using shell script to analyze the results
Create a file named input.g_rms. write the group number in this file. In your shell script after command line write input.g_rms. when the command is executed in shell the file input.g_rms having group number will be read. Hope it works. Shahid nayeem On Fri, Feb 10, 2012 at 4:19 PM, Kiwoong Kim ilmare...@gmail.com wrote: Hi, I'm not good at shell programming now. For the simplicity, I wrote down all the gromacs commands in one shell script. It means that if I execute the .sh file, then every works including graphs used for analysis are done. However, when there are g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm, I have to select the groups manually. This is quite inconvenient... Is there any way to handle this?? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Running_crashed_run
Dear all I am using Gromacs-4.5.4 . when I restart a crashed run after generating a new .tpr with tpbconv ,it does not run without giving the option of -noappend. How to run this with -append option. as far as I know in all version of 4.x onward -append is default option but it does not works in my case. Thanks for any help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tip3p water in gromacs_4.5.4
Dear all I want to use tip3p water model for solvating my protein with genbox command . I couldnt find tip3p.gro file in Gromacs/share/top folder . please help me I am following using command genbox -cp protein_box.gro -cs tip3p.gro -o solv.gro -p *.top It says tip3p.gro not found. Please help. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topology and parameter for cobalt metal
Dear all I am interested in simulating a model protein with cobalt forming coordinate bond with His. I coud'nt find entry for cobalt in any forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD
Thanks. But in timeline plugin of VMD I am able to measure RMSD with respect to one of the frame of trajectory and I am interested to measure RMSD with respect to another molecule. I am trying to measure RMSD of trajectory frames with respect to Bound and unbound configuration of molecule so that I can compare side chain configuration of trajectory with bound and unbound sidechain configuration. Please help. Shahid Nayeem On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl felmer...@uchile.clwrote: In any case, if you really want to see flexibility then you need RMSF and not RMSD as the later will only tell you about how similar is the configuration of a sidechain compared to a reference frame. If that is still what you want i think VMD has a tool for that in the timeline plugin. regards Felipe Mensaje original De: gianluca.sant...@ibs.fr Fecha: 15-nov-2011 10:18 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote: Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem Try g_rmsf -res , it could be useful, maybe. -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RMSD
Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] protein_model_refinement
Dear All I am trying to refine a protein model which is a homodimer with each chain having 609 residues.I tried minimizing in Chimera and then checking models with procheck.Infact model quality deteriorated as far as Ramachandran plot is concerned. Will doing MD simulation help me in Gromacs. It is a big protein so long MD simulation is not possible. Short duration MD will be insufficient to search native structure. I am stuck-up. Can anyone on this list help me. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Protein_model_refinement
Dear All I want to refine a protein homology model, I did minimization but then procheck does not give better Ramachandran plot. This model is a homodimer with each chain of 609 residue and a total of 1218 residue so a long MD simulation to search native state is not feasible. Can any one help me on this list to tell that how should I attempt this problem. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Arginine_Hydrochloride topology
I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Arginine_Hydrochloride topology
I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box shahid nayeem On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/**Documentation/How-tos/**Multiple_Chainshttp://www.gromacs.org/Documentation/How-tos/Multiple_Chains . Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp
Re: [gmx-users] Arginine_Hydrochloride topology
Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pmf_calculation
I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. shahid Nayeem On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear Justin I did some more sampling and sending you profile.xvg, histo.xvg. and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my the difference in profile.xvg and hist.xvg. Both should be same but I get different curves here. I can't tell you the difference because you haven't shown how they were generated. My blind guess is that hist.xvg (a very confusing name for a PMF profile) was generated from data that have poor sampling in two regions. The contents of profile.xvg look normal. I don't know which of these curves corresponds to histo.xvg, because the histograms therein look fine. Please make sure to give full descriptions of these files. You've quote a message that is over a month old. I've replied to hundreds of messages since then and I do not remember the full context of our discussion. -Justin On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: Dear Justin I did pmf calculation for my protein-protein complex using your tutorial.Off course changing the pull_direction suitable for my protein but more or less following the same strategy. I am using gromacs_4.5.4 and g_wham utility. The profile.xvg file which I get is attached and it shows two dips in PE curve. Please see it and tell me why I am getting these dips. You have insufficient sampling in at least these two regions. Your histograms should confirm this. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pmf_calculation
Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. An identical command with identical input files producing totally different output? Sorry, but I find that hard to believe. Check your work and make sure you're using the input you think you are. I suspect something's amiss and you're not seeing it. -Justin shahid Nayeem On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: Dear Justin I did some more sampling and sending you profile.xvg, histo.xvg. and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my the difference in profile.xvg and hist.xvg. Both should be same but I get different curves here. I can't tell you the difference because you haven't shown how they were generated. My blind guess is that hist.xvg (a very confusing name for a PMF profile) was generated from data that have poor sampling in two regions. The contents of profile.xvg look normal. I don't know which of these curves corresponds to histo.xvg, because the histograms therein look fine. Please make sure to give full descriptions of these files. You've quote a message that is over a month old. I've replied to hundreds of messages since then and I do not remember the full context of our discussion. -Justin On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear Justin I did pmf calculation for my protein-protein complex using your tutorial.Off course changing the pull_direction suitable for my protein but more or less following the same strategy. I am using gromacs_4.5.4 and g_wham utility. The profile.xvg file which I get is attached and it shows two dips in PE curve. Please see it and tell me why I am getting these dips. You have insufficient sampling in at least these two regions. Your histograms should confirm this. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org mailto:gmx-users-request@__gr**omacs.org http://gromacs.org mailto:gmx-users
[gmx-users] Adding_topology_aminoacid
Dear All I am solvating my protein in a cubical box with a .gro file containing water and one amino acidX. when I run grompp I get error No such moleculetype aminoacidX . Should I create de novo .itp file for the amino acidX on proDrg because I tried to include ffbonded.itp and ffnonbonded.itp in .top file but this also gives error in grompp. Creating a new .itp file on ProDrg will again cause problem of charge and parametrization. Since it is individual normal amino acid not present in protein but as insert molecule in solvation box so I think creating new .itp file should not be needed. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Arginine_Hydrochloride topology
Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pmf_calculation
Dear Justin I did pmf calculation for my protein-protein complex using your tutorial.Off course changing the pull_direction suitable for my protein but more or less following the same strategy. I am using gromacs_4.5.4 and g_wham utility. The profile.xvg file which I get is attached and it shows two dips in PE curve. Please see it and tell me why I am getting these dips. Shahid Nayeem profile.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pmf_calculation
Dear Justin Here is my histogram file which does not show any window overlap. The sampling window I choose was 0.2 nm which I think is very large. Please suggest. Shahid nayeem hist.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Thermal_Unfolding
Dear Gromacs Users I want to study thermal unfolding of protein in gromacs. One way to do is to simulate at different temperature. What I want to do is to gradually increase temperature after each n number of steps and collect the n' number of frame for each temperature interval. If I can do this in gromacs then what should be the .mdp file for such increment in temperature at regular intervals. Thanks for any help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] binding_affinity
Hi Justin Before trying for my system I am trying to learn running these simulation with the help of your tutorial. The only change I made is that I applied pull_code for 2nm movement only in order to save time. Thereafter, with trjconv I generated all 200 conf.gro. when I run your perl script it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] binding_affinity
Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] binding_affinity
Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] binding_affinity
Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rms and g_cluster
Hi Justin If I make an index group with backbone and CA C N O group of the concerned residues and then do least square fitting then do this fitting is equivalent to backbone fitting first and then translating to coincide CA of the residue of interest. Is there any other programme developed for gromacs trajectory analysis where I can do backbone fitting first and then translate to coincide CA of residue of interest before calculating RMSD. Shahid Nayeem On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I want to calculate RMSD of one side chain residue from simulation trajectory after full backbone alignment as well as translating to coincide CA of the residue of interest. Is it possible to do with g_rms both backbone alignment as well as translating to coincide CA. Least-squares fitting is performed on whatever group you choose (i.e. backbone), and the calculation group can then be whatever you want. You can use trjconv to do translational fitting, but I don't know that you can force g_rms to always align this certain atom and still perform a backbone fit; these two may work against one another, even if the difference is small. Another clarification is that in gromacs g_cluster how can I use greedy algorithm for clustering. What is a greedy algorithm? The available methods are described in the manual and/or g_cluster -h. -Justin Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rms and g_cluster
Dear All I want to calculate RMSD of one side chain residue from simulation trajectory after full backbone alignment as well as translating to coincide CA of the residue of interest. Is it possible to do with g_rms both backbone alignment as well as translating to coincide CA. Another clarification is that in gromacs g_cluster how can I use greedy algorithm for clustering. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] backbone_few_sidechain_fixed
Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ; By user: shahid (511) ; On host: coe.iitd.ac.in ; At date: Thu Feb 17 17:52:59 2011 ; ; This is your topology file ; They Paint Their Faces So Differently From Ours (Gogol Bordello) ; ; Include forcefield parameters #include ffG43a1.itp ; Include A-chain topologies #include complex_A.itp #include complex_B.itp #include complex_C.itp #ifdef POSRES #include posreA.itp #include posreB.itp #include posreC.itp #endif If I keep only one posreA.itp then grompp runs without error but if I use all three or two posre.itp it gives following error. Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 1275 Fatal error: [ file posreB.itp, line 118 ]: Atom index (968) in position_restraints out of bounds (1-966). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. I separated including topology and defining posres in three different parts but even then it gives error and grompp fails. In my posre.itp generated by genrestr I selected a group containing backbone and some side chains. My Idea is to keep the backbone as well as side chain of all the residues which are not on interface fixed and allow free movement of only interface residue and then run full MD. For above procedure I defined define = POSRES in full.mdp Please suggest what should I do . For a single chain I did MD keeping backbone fixed and allowing side chain free movement. In my posres.itp I used a force of 2000 kj to keep them in fixed position with option genrestr -fc. Waiting for reply Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] server_for_Gaussian
Dear All If any one is aware of a server on which one can upload job for running Gaussian, Please let me know. This I need to modify charges in the topology file created by ProDrg server. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box_preparation
Hi Justin Thanks a lot. I tried doing energy minimization and th lowering emtotal to 200 and the system converged to Steepest Descents converged to Fmax 200 in 1411 steps Potential Energy = -3.9063050e+05 Maximum force = 1.3442458e+02 on atom 927 Norm of force = 1.4758101e+01 For equilibration of solvation box I am following a biophys j paper in which protocol for urea box preparation is given. A simulated annealing under high pressure (ref_p=100) to cool system from 300 to 0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same condition. If this way is harsh treatment of system then suggest me the way out. My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp are attached with this mail Shahid Nayeem On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box PRODRG doesn't have a problem of missing charges. It provides notoriously incorrect charges. with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the These settings make no sense. An emtol of 2000 is very high, and emstep of 3000 is total nonsense. How well did you EM converge? What were the values of the potential energy and maximum force? gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. How about simplifying the problem. Does the system run under normal conditions? In other words, can you run normal MD? You're treating the system very harshly with the combination of high pressure and annealing. Without seeing your .mdp file for this process, it's impossible to say how reasonable your settings are. It is also possible that your parameters for CHAPS (if they are the default ones from PRODRG) are incorrect. The charges and charge groups nearly always are. Without seeing them, there's nothing better to offer. -Justin shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. You've set up a system that isn't stable, but we don't have enough information to have any idea why. I tried with new box size doesn't go close to describing your method in enough detail for anyone to know where you went wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic tips Mark Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkuljalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed
[gmx-users] interface_enrgy
Dear User I am doing MD on protein complex keeping backbone as well as side chain of all residues which is not on th interface fixed. For this I prepared posre_backbone_sidechain.itp and defined this in .top file for full MD. Now I want to know from the trajectory the best side chain conformation of the interface residues for which I want to see the change in total energy of the interface residues throught the trajectory. I prepared index file for interface residues. But g_energy command does not takes -n index.ndx to calculate energy of these groups. How can I do that. Please suggest. Thanking you Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] interface_enrgy
That means in energy group in .mdp file I should write interface.ndx and tell me if on interface there is hydrogen bond then its value I will get or not. Shahid Nayeem On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear User I am doing MD on protein complex keeping backbone as well as side chain of all residues which is not on th interface fixed. For this I prepared posre_backbone_sidechain.itp and defined this in .top file for full MD. Now I want to know from the trajectory the best side chain conformation of the interface residues for which I want to see the change in total energy of the interface residues throught the trajectory. I prepared index file for interface residues. But g_energy command does not takes -n index.ndx to calculate energy of these groups. How can I do that. Please suggest. You can set energygrps in the .mdp file and use mdrun -rerun to re-calculate the components of the nonbonded interaction energy between different groups. You cannot decompose the total energy or bonded terms. If you've used PME, the long-range term cannot be decomposed, either. -Justin Thanking you Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box_preparation
Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. You've set up a system that isn't stable, but we don't have enough information to have any idea why. I tried with new box size doesn't go close to describing your method in enough detail for anyone to know where you went wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic tips Mark Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkuljalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a similar situation while If your box was not completely solvated, then don't use -maxsol. A box of 6x6x6 nm should require more than 500 molecules of water to fill. If you're trying to achieve some specific mole fraction or concentration, then re-figure your box size. -Justin preparing 10M urea salvation box. This was followed by 1ns simulated annealing from temp 300K to 0K and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support
[gmx-users] solvation_box_preparation
Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a similar situation while preparing 10M urea salvation box. This was followed by 1ns simulated annealing from temp 300K to 0K and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box_preparation
Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a similar situation while If your box was not completely solvated, then don't use -maxsol. A box of 6x6x6 nm should require more than 500 molecules of water to fill. If you're trying to achieve some specific mole fraction or concentration, then re-figure your box size. -Justin preparing 10M urea salvation box. This was followed by 1ns simulated annealing from temp 300K to 0K and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] solvation_box
Dear All I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box
Hi Mark Thanks. I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I solvated this box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur and I got water in one region and chaps molecule spread throughout box but not inside water. I should have visualized it earlier before going for minimization. Please help me. shahid Nayeem On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/27/11, *shahid nayeem * msnay...@gmail.com wrote: Dear All I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. You haven't told us how you've solvated the system (e.g. with genbox), that it looked OK when you visualized it between each step, and that you're sure your observations cannot be rationalized as a periodicity artefact. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] solvation_box
I forgot to mention that when I prepared urea_water box then also I got similar box of water in one region and urea in other region separated from it. But on minimization and following simulated annealing and equilibration I got a uniformly mixed urea water box. Shahid Nayeem On Thu, Jan 27, 2011 at 12:30 PM, shahid nayeem msnay...@gmail.com wrote: Hi Mark Thanks. I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I solvated this box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur and I got water in one region and chaps molecule spread throughout box but not inside water. I should have visualized it earlier before going for minimization. Please help me. shahid Nayeem On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/27/11, *shahid nayeem * msnay...@gmail.com wrote: Dear All I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. You haven't told us how you've solvated the system (e.g. with genbox), that it looked OK when you visualized it between each step, and that you're sure your observations cannot be rationalized as a periodicity artefact. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] preparation_solvation_box
Dear Gmx User I want to prepare a solvation box for say 50mM chaps solution. The density is not known. How should I start calculating the number of chaps molecule and number of water molecule required for say 6X6X6 size box, which after equilibriation should give the exact strength of the solution. For Urea and guanidinium I know the references and mail archive has many suggestion but how I should proceed with this new solvation box. msnayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Interaction_between_protein_small_molecule
Dear Gromacs Users I wanted to study the interaction between a small molecule and protein. I prepared the system by inserting small molecule -nmol and protein by genbox and then I solvated it with water. when I tried to do PR dynamics it started giving many LINC WARNINGS. I reduced the time of equilibration and then PR run was completed without any warning. When I used production run it started giving LINC warning.Even after setting GMX_MAXCONSTRWARN to -1 I am getting LINC warning and programme termination with fatal error. Instead of simple docking I want to do MD with GROMACS to see interaction between the two molecule. Please suggest me, how can I do this. Thanking you. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Terminal_ARG_residue causing problem in pdb2gmx
Dear Gromacs User My pdb is homodimer with Arg as c-terminal residue. With this pdb I am etting following error in pdb2gmx command Program pdb2gmx, VERSION 4.0.7 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms while sorting atoms The command executed is as follows pdb2gmx -f.pdb -o.gro -p .top I tried to change the OXT atom name in pdb file to O2, then also I am getting the same error. In .rtp entry there is ARG residue as N-ter but for C-ter ARG there is no residue. Please suggest. Waiting for helps from gromacs users. Shahid Nayem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] heme
Hi Erik I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD, angles e.g. NR (HIS) FE SD(MET) and dihedral angle CH2(MET) SD (MET) FE NR(HIS) is missing in this force field. hence I am getting error while running grompp. Please suggest me what should I do. Shahid Nayeem On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund er...@xray.bmc.uu.se wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] heme
Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] heme
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since a long time ago, but I am sure problems exist in recent versions. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] following_change_native_contact
Dear All How can I follow the changes in native contacts of protein unfolding trajectory. Is it g_mdmat, if so then how to analyze the results obtained from this command. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Heme_Grompp_error
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Heme_Grompp_error
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Grompp error: No default g96angle type
HI I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives any eror using ffG43a1. .top file produced shows all bonds (Fe SD of MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error lines does not have bond/angle nomenclature such as 809 810 2gb_30 810 811 2gb_29 810 1068 2 812 813 2gb_4 812 814 2gb_9 814 815 2gb_2 810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp file of force-field and adding these bonds and giving some name to it but got the same error in grompp. Though .top file shows these bonds the .gro file generated does not show these bonds in VMD while original pdb file shows these bonds. thanking you. waiting for your suggestion. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. One of the most important choices when conducting MD simulations is the force field. You'll have to find one that works. It appears that (unfortunately) the Gromos force fields do not work out of the box when heme is involved. If you want specific advice about other force fields, you'll have to describe your problem much better than gives error at some point. No one can help you sort that out. You'd do well to look into the literature. Simulations of heme proteins are not novel, so clearly others have made this work, and in some cases, parameters might be provided for the terms that are missing. -Justin shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
[gmx-users] Heme_Grompp Error
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Grompp error: No default g96angle type
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. Thanks in anticipation of help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Grompp error: No default g96angle type
Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas
Dear All Using g_sas on trajectory file with command g_sas -f .xtc -s .tpr -oa atomarea.xvg gives following output @title Area per atom @xaxis label Atom # @yaxis label Area (nm\S2\N) @TYPE xy 1 0.139885 0.0351154 2 0.0510893 0.0236223 3 0.0510077 0.0234374 4 0.0512037 0.0234554 5 0.0284763 0.0401088 6 0.236609 0.108979 Tghe first column is atom no. and what are the values in two columns. I want average solvent accessible surface area of each atom of my protein in whole trajectory. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] do_dssp
Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
Hi Justin I choose group 5 main chain for dssp calculation Shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
Hi No i dont have any capping group shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I choose group 5 main chain for dssp calculation Do you have any capping groups (N-acetyl, C-amine, etc)? -Justin Shahid Nayeem On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] DSSP
Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xmgrace
Dear all I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands. tar -xvzf xmgr-4.1.2.tar.gz cd xmgr-4.1.2 ./configure make make install But it gives error command xmgr not found. Please help. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein Aggregation using Gromacs
Dear all What are the analysis tools which should be used on MD trajectory file in order to find potential aggregation sites of a protein. Anyone can tell me about specific resource material on use of Gromacs to predict protein aggregation hot spots from MD trajectory anlysis. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
Hi I have used TANGO Aggrescan, Zyggregator and other online tools but I am unable to find and pinpoint residue responsible for aggregation. Then I did MD simulation of the proteins with gromacs at different temperature. Now in this background I need suggestion to analyse my MD trajectory. shahid Nayeem On 5/12/10, Ran Friedman r.fried...@bioc.uzh.ch wrote: Hi, There's no recipie to locate aggregation hot spots based on MD simulations. There are many papers on simulations of protein and peptide aggregation from which you can draw some ideas, but bear in mind that aggregation of more than very few and very small peptides is typically much slower than what one can simulate using atomistic MD. For a quick approach you can use sequence analysis tools, e.g., TANGO http://tango.crg.es/ Good luck, Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- shahid nayeem wrote: Dear all What are the analysis tools which should be used on MD trajectory file in order to find potential aggregation sites of a protein. Anyone can tell me about specific resource material on use of Gromacs to predict protein aggregation hot spots from MD trajectory anlysis. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] confusion about trjconv
Dear all when I do long mdrun and the run crashes, I generate new .tpr file to restart the run. Sometime in order to complete run two or three such .tpr file is generated after reading previous .trr and .ene files. After completion of the run when I use trjconv (after combining .trr files with trjcat) which .tpr file should be used with -s flag the first .tpr file which is generated with grompp at the start of mdrun or the last .tpr file generated by tpbconv reading previous .trr and .ene file. I know that in recent version of gromacs restart can be done using mdrun supplying .cpt file with -cpi flag. I require answer of my question regardless of the use of .cpt file. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Shahid On 4/23/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file Energy minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no Position_restraint.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds constraintalgorithm = LINCS integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Full_MD.mdp cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1 ps. nstcomm = 1 nstxout = 5000 nstvout = 4 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 500 500 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 500 K. gen_vel = no gen_temp = 500.0 gen_seed = 173529 shahid On 4/27/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. -Justin Shahid On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help
Re: [gmx-users] more than one peptide in one simulation box
Hi Justin Should I try to do position restraint at 500k and then full MD simulation. shahid On 4/27/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file snip ref_t = 300 300 Here, you're equilibrating at 300 K... snip ref_t = 500 500 and here, you're running MD at 500 K, without any equilibration in between. That could be a problem, but more likely, the high temperature is simply causing the structure to break down. Short helices are usually not stable in isolation, and heating them to extreme conditions will probably accelerate this process. The various results you're seeing with different helices may just reflect that you haven't simulated long enough to see convergence in the structural features, but from what you've described, I expect what you're seeing is entirely normal, and almost predictable. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. Shahid On 4/27/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. Indeed. MD is chaotic, and there's no reason to expect all peptides of any length to show the same actual behaviour in a trajectory. They might show the same behaviour in the limit of a converged ensemble, but only if aggregation is not a factor. Mark On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] more than one peptide in one simulation box
Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox
I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. msnayeem On 4/20/10, Justin A. Lemkul jalem...@vt.edu wrote: fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong. I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. That works. Glad you found a solution. -Justin Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
