Re: [gmx-users] Gromacs Installation problem
Thanks Mark. Your guess is right. It works. Regards, Shankar On Fri, Jan 9, 2015 at 7:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Last time I saw something like that, the person was trying to build in and install to the same place. Sharing your cmake command line would have been a good idea. Mark On Jan 9, 2015 2:27 PM, Shankar Prasad Kanaujia spkanau...@gmail.com wrote: Dear Users, I am getting a unique problem while installing gromacs. I am able to install any version of gromacs in the default path (i.e. /usr/local/gromacs). However, if I specify any other location by -DCMAKE_INSTALL_PREFIX=/home/user/softwares/GMX_5.0.4, I get the following error: !-- CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /home/user/softwares/GMX_5.0.4/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) -- at the last step (i.e. make install). I tried almost everything available through Google search. I have tried with several versions of cmake both as root as well as user. I would really appreciate if any one can provide some hint to solve this problem. Regards, Shankar -- Shankar Prasad Kanaujia, Ph.D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati - 781039 Assam, India Tele: 0361 258 2228 Fax: 0361 258 2249 Email: spkanau...@iitg.ernet.in Homepage: http://www.iitg.ernet.in/spkanaujia/ -- 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. -- Shankar Prasad Kanaujia, Ph.D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati - 781039 Assam, India Tele: 0361 258 2228 Fax: 0361 258 2249 Email: spkanau...@iitg.ernet.in Homepage: http://www.iitg.ernet.in/spkanaujia/ -- 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] Gromacs Installation problem
Dear Users, I am getting a unique problem while installing gromacs. I am able to install any version of gromacs in the default path (i.e. /usr/local/gromacs). However, if I specify any other location by -DCMAKE_INSTALL_PREFIX=/home/user/softwares/GMX_5.0.4, I get the following error: !-- CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /home/user/softwares/GMX_5.0.4/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) -- at the last step (i.e. make install). I tried almost everything available through Google search. I have tried with several versions of cmake both as root as well as user. I would really appreciate if any one can provide some hint to solve this problem. Regards, Shankar -- Shankar Prasad Kanaujia, Ph.D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati - 781039 Assam, India Tele: 0361 258 2228 Fax: 0361 258 2249 Email: spkanau...@iitg.ernet.in Homepage: http://www.iitg.ernet.in/spkanaujia/ -- 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] Atomtype ZN2+ not found
Dear users, I had simulated one protein with metal Zn (Zinc) bound using Gromacs version 4.5.5 with OPLSS-AA force field. Now, I am trying to rerun to calculate the energy between two groups with Gromacs version 5.0.2. I am getting the following error: Atomtype ZN2+ not found. Can anybody help me out. Thanking you. Regards, Shankar -- 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] Atomtype ZN2+ not found
Dear Justin, Thanks for the details. As you mentioned, I did not find any force field which contains parameters for all metals. Regards, Shankar On Fri, Dec 19, 2014 at 5:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/14 2:59 AM, Shankar Prasad Kanaujia wrote: Dear users, I had simulated one protein with metal Zn (Zinc) bound using Gromacs version 4.5.5 with OPLSS-AA force field. Now, I am trying to rerun to calculate the energy between two groups with Gromacs version 5.0.2. I am getting the following error: Atomtype ZN2+ not found. Zn2+ and some other ions were removed from the OPLS-AA files because they were not, in fact, actually OPLS-AA parameters. Note that this is stated prominently in ffnonbonded.itp: ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins or tutorial Argon simulations we have added them. Cu2+ Cu2+ 29 63.54600 2.000 A2.08470e-01 4.76976e+00 Fe2+ Fe2+ 26 55.84700 2.000 A2.59400e-01 5.43920e-02 Zn2+ Zn2+ 30 65.37000 2.000 A1.95200e-01 9.78219e-01 Ar Ar 18 39.94800 0.000 A3.41000e-01 2.74580e-02 I would rigorously evaluate whatever you did with 4.5.5 and consider repeating the simulations with better parameters, if they exist, or using a force field for which Zn2+ has been parametrized properly. -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. -- Shankar Prasad Kanaujia, Ph.D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati - 781039 Assam, India Tele: 0361 258 2228 Fax: 0361 258 2249 Email: spkanau...@iitg.ernet.in Homepage: http://www.iitg.ernet.in/spkanaujia/ -- 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.
