[gmx-users] sigma and epsilon values for C and H atoms in CNT
Hi all, Can any one please share the values of sigma and epsilon for both C and H atoms in a CNT (for Charmm27 forcefield)? Thanks! Sanchaita. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Charmm27 forcefield parameters for carbon nanotubes
Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the "modeling carbon nano-tubes with gromacs" (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa forcefield. I have tried in a similar way but is having difficulty in getting the charmm27 forcefield parameters for carbon nanotubes. If somebody has done such kind of simulation, kindly share the parameters. Thanks, Sanchaita. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CHARMM forcefield parameters for carbon naotubes
Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the modeling carbon nano-tubes with gromacs (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa forcefield. I have tried in a similar way and I keep getting errors: --- Opening force field file ./test.ff/ffcharmm.n2t There are 5 name to type translations in file ./test.ff Generating bonds from distances... atom 80 There are 1 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) --- If anyone has done the simulation of a CNT using CHARMM27 forcefield then please help. Thank you. Regards, Sanchaita. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs in UBUNTU
I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try
Re: [gmx-users] Gromacs in UBUNTU
definitely yes.. Then only I came to know about this gmx solvant... else How could I? my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website
Re: [gmx-users] Gromacs in UBUNTU
Thanks Marks and really sorry for all trouble because of my stupid understanding... On 18 May 2015 at 20:58, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Use gmx_mpi solvate. You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS versions only because those are magically transformed into things like gmx_mpi pdb2gmx, to provide a year of backwards compatibility. But providing backwards compatibility for a new name was not really a good thing to do, so there is no solvate_mpi. GROMACS 5.1 will remove the old-style names without gmx prefixes, so people need to start getting used to using the gmx prefix (or learn to roll their own symlinks). Mark On Mon, May 18, 2015 at 5:19 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses
Re: [gmx-users] Gromacs in UBUNTU
Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs in UBUNTU
sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un
Re: [gmx-users] Gromacs in UBUNTU
Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation of heme along with h2o2
Hi, I tried using charmm forcefield to simulate heme but we are getting warning messages. WARNING: atom HA is missing in residue HEME 1500 in the pdb file . . . for all 30 hydrogens. Later we tried modifying the aminoacids.hdb as: HEME3 1 5 HA CA N C CB 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ But the problem still persists. What should be done?? Please help. regards, Sanchaita. On 19 February 2015 at 09:43, Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear Justin, thank you for the reply. However, I would like to know if there is any server which can generate parameters for heme to be used in OPLS-aa? We have already tried in swissparam with failed results. Please help. On 18 February 2015 at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. SwissParam creates CHARMM-compatible parameters, so no, you can't mix those with GROMOS. CHARMM supports heme, but you have to clean up a lot of auto-generated angles and dihedrals that don't belong. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation of heme along with h2o2
Dear Justin, thank you for the reply. However, I would like to know if there is any server which can generate parameters for heme to be used in OPLS-aa? We have already tried in swissparam with failed results. Please help. On 18 February 2015 at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. SwissParam creates CHARMM-compatible parameters, so no, you can't mix those with GROMOS. CHARMM supports heme, but you have to clean up a lot of auto-generated angles and dihedrals that don't belong. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simulation of heme along with h2o2
Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. Thanks in advance. Sanchaita. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] query regarding automated topology builder and repository
Dear all, I would like to know if automated topology builder and repository server http://compbio.biosci.uq.edu.au/atb/index.py?tab=existing_tabnocache=836 gives the correct topology for ligands? For e.g. I have to build topology for triclosan and it is present in this repository. But the total charge on the charge group is not 0.00. For e.g. - [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 H1_NNX H710.463 1.0080 2OA1_NNXO161 -0.558 15.9994 ; -0.095 3OE1_NNX O72 -0.395 15.9994 4HC1_NNX H420.191 1.0080 5 C1_NNXC1220.225 12.0110 6 C1_NNX C82 -0.312 12.0110 7 C1_NNX C720.291 12.0110 ; -0.000 8CL1_NNX CL143 -0.080 35.4530 9 C1_NNX C43 -0.277 12.0110 10 C1_NNX C330.552 12.0110 ; 0.195 11CL1_NNX CL154 -0.093 35.4530 12 C1_NNX C64 -0.163 12.0110 13 C1_NNX C540.138 12.0110 14HC1_NNX H340.118 1.0080 ; 0.000 15 C1_NNX C25 -0.442 12.0110 16HC1_NNX H250.207 1.0080 17HC1_NNX H150.138 1.0080 18 C1_NNX C150.097 12.0110 ; 0.000 19HC1_NNX H660.152 1.0080 20 C1_NNXC116 -0.252 12.0110 ; -0.100 21HC1_NNX H570.157 1.0080 22CL1_NNX CL177 -0.096 35.4530 23 C1_NNXC107 -0.004 12.0110 24 C1_NNX C97 -0.057 12.0110 ; -0.000 ; total charge of the molecule: -0.000 --- Do I need to modify it before doing the simulation or use it as it is? Thanks. Sanchaita. -- SANCHAITA RAJKHOWA, Research Scholar, C/O Prof. Ramesh C. Deka, Department of Chemical Science, Tezpur University, Napaam, Tezpur-784 028 ___ D I S C L A I M E R This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom labeling in forcefield file and pdbaredifferent
Hii, Thank you Justin for the help. I could successfully rename the atoms. The crystal structure of my protein does not have any hydrogens in it but still it is showing missing hydrogen atoms. I tried using -ignh command but still can't fix this. Please help. WARNING: atom AH61 is missing in residue NADH 301 in the pdb file WARNING: atom AH62 is missing in residue NADH 301 in the pdb file WARNING: atom AH2* is missing in residue NADH 301 in the pdb file WARNING: atom AH3* is missing in residue NADH 301 in the pdb file WARNING: atom NH71 is missing in residue NADH 301 in the pdb file WARNING: atom NH72 is missing in residue NADH 301 in the pdb file WARNING: atom NH2* is missing in residue NADH 301 in the pdb file WARNING: atom NH3* is missing in residue NADH 301 in the pdb file Fatal error: There were 8 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing What should I do?? On 4/6/14, 10:29 AM, Sanchaita Rajkhowa wrote: Hii, I understand renaming the atoms in the coordinate file but how do I do the one-to-one mapping of the atoms?? Which atom in the pdb file represnt AP or AO5* in the forcefield file? The N prefix indicates atoms belonging to the nicotinamide nucleotide, A is for adenosine. Atoms in gromos96 forcefield file- [ NADH ] [ atoms ] AP P 0.76000 0 AO1POM-0.63500 0 AO2POM-0.63500 0 AO5*OA-0.36000 0 O3POA-0.26000 1 NP P 0.76000 1 NO1POM-0.63500 1 NO2POM-0.63500 1 NO5*OA-0.36000 1 AC5* CH2 0.0 2 AC4* CH1 0.16000 3 AO4*OA-0.36000 3 AC1* CH1 0.2 3 . . . Atoms in pdb file- PA NAD A 301 19.488 11.324 16.304 1.00 33.61 P O1A NAD A 301 20.484 12.030 15.464 1.00 34.53 O O2A NAD A 301 19.206 12.087 17.539 1.00 30.85 O O5B NAD A 301 19.972 9.804 16.571 1.00 32.18 O C5B NAD A 301 20.526 8.977 15.561 1.00 32.62 C C4B NAD A 301 21.503 7.982 16.198 1.00 31.90 C O4B NAD A 301 22.185 7.163 15.252 1.00 31.32 O C3B NAD A 301 22.594 8.724 16.954 1.00 31.17 C O3B NAD A 301 22.425 8.501 18.330 1.00 30.69 O C2B NAD A 301 23.888 8.185 16.376 1.00 30.92 C O2B NAD A 301 24.938 8.072 17.309 1.00 32.63 O C1B NAD A 301 23.424 6.848 15.845 1.00 30.98 C N9A NAD A 301 24.416 6.284 14.931 1.00 30.18 N You will have to visualize the structure to determine what A and B represent (either adenosine or nicotinamide), then map that back to the NADH nomenclature in the force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- SANCHAITA RAJKHOWA, Research Scholar, C/O Prof. Ramesh C. Deka, Department of Chemical Science, Tezpur University, Napaam, Tezpur-784 028 ___ D I S C L A I M E R This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom labeling in forcefield file and pdb aredifferent
Hii, I understand renaming the atoms in the coordinate file but how do I do the one-to-one mapping of the atoms?? Which atom in the pdb file represnt AP or AO5* in the forcefield file? Atoms in gromos96 forcefield file- [ NADH ] [ atoms ] AP P 0.76000 0 AO1POM-0.63500 0 AO2POM-0.63500 0 AO5*OA-0.36000 0 O3POA-0.26000 1 NP P 0.76000 1 NO1POM-0.63500 1 NO2POM-0.63500 1 NO5*OA-0.36000 1 AC5* CH2 0.0 2 AC4* CH1 0.16000 3 AO4*OA-0.36000 3 AC1* CH1 0.2 3 . . . Atoms in pdb file- PA NAD A 301 19.488 11.324 16.304 1.00 33.61 P O1A NAD A 301 20.484 12.030 15.464 1.00 34.53 O O2A NAD A 301 19.206 12.087 17.539 1.00 30.85 O O5B NAD A 301 19.972 9.804 16.571 1.00 32.18 O C5B NAD A 301 20.526 8.977 15.561 1.00 32.62 C C4B NAD A 301 21.503 7.982 16.198 1.00 31.90 C O4B NAD A 301 22.185 7.163 15.252 1.00 31.32 O C3B NAD A 301 22.594 8.724 16.954 1.00 31.17 C O3B NAD A 301 22.425 8.501 18.330 1.00 30.69 O C2B NAD A 301 23.888 8.185 16.376 1.00 30.92 C O2B NAD A 301 24.938 8.072 17.309 1.00 32.63 O C1B NAD A 301 23.424 6.848 15.845 1.00 30.98 C N9A NAD A 301 24.416 6.284 14.931 1.00 30.18 N . . . Thanks. On 4/4/14, 4:46 AM, Sanchaita wrote: Hi, I am trying to perform the simulations of a particular protein having NADH as a cofactor. However, when I try to run pdb2gmx command it shows an error. It seems that the gromos96 43a2 force field has parameters for NADH but the labeling do not match the labeling done in the pdb file. What do I do? Please help. Rename the atoms in the coordinate file to match the expectations of the .rtp file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- SANCHAITA RAJKHOWA, Research Scholar, C/O Prof. Ramesh C. Deka, Department of Chemical Science, Tezpur University, Napaam, Tezpur-784 028 ___ D I S C L A I M E R This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
