Yes, I have introduced the new .rtp entry in /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. What could be wrong?
----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Monday, September 30, 2013 11:16:57 AM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 12:50 PM, Ehsan Sadeghi wrote: > Thanks Justin, > > I modified the pdb file, but it cannot recognize my residue LIG. Here is the > error: > > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b > Reading nafion5.pdb... > Read 46 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 2 residues with 46 atoms > > chain #res #atoms > 1 ' ' 2 46 > > All occupancies are one > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (gromos53a6) > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp > Using default: not generating all possible dihedrals > Using default: excluding 3 bonded neighbors > Using default: generating 1,4 H--H interactions > Using default: removing proper dihedrals found on the same bond as a proper > dihedral > Residue 108 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb > > Back Off! I just backed up topol.top to ./#topol.top.41# > Processing chain 1 (46 atoms, 2 residues) > Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA. > Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA. > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.6.3 > Source code file: > /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 > > Fatal error: > Residue 'LIG' not found in residue topology database > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > You have introduced the new .rtp entry in the correct file, right? That is, you have modified /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp? -Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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/Mailing_Lists
