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 time 0.000 1297343010 Segmentation fault Why is this happening? Thanks, Anirban On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh < [email protected]> 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 <[email protected]>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 >> <[email protected]> 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 [email protected] >> > 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 [email protected]. >> > 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 list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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