[gmx-users] Error: No such moleculetype Protein
Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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] Error: No such moleculetype Protein
Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Error: No such moleculetype Protein
Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Error: No such moleculetype Protein
Hi, I have worked around the problem. I was not including a .itp file. But now I am getting Segmentation Fault: Excluding 1 bonded neighbours for DSPC 104 Excluding 1 bonded neighbours for W 1397 Excluding 1 bonded neighbours for NA+ 0 Excluding 1 bonded neighbours for CL- 4 Number of fg atoms 410288 Number of cg atoms 57296 Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms. Reading frame 0 time0.000 1297343010 Segmentation fault Why is this happening? Thanks, Anirban On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
