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 ------------------------------------------------------- Thanks, Ehsan ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Friday, September 27, 2013 5:50:00 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 8:43 PM, Ehsan Sadeghi wrote: > Thanks for your prompt response. I made the modifications on the > aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff. > > I did not modify any force field. I thought I still can use the default force > field in gromos; isn't it right? Yes you did; you modified the Gromos96 53A6 force field. There's nothing wrong with that; it's precisely what you wanted to do. Also note that there is no such thing as a default force field. > Here is the output from pdb2gmx. Thank you for your consideration. > > ----------------------------------- > > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b > Reading nafion3.pdb... > WARNING: all CONECT records are ignored > Read 46 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 2 chains and 0 blocks of water and 0 residues with 46 atoms > > chain #res #atoms > 1 'G' 1 24 > 2 'H' 1 22 > > > WARNING: there were 1 atoms with zero occupancy and 45 atoms with > occupancy unequal to one (out of 46 atoms). Check your pdb file. > > 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.36# > Processing chain 1 'G' (24 atoms, 1 residues) > Warning: Starting residue LI0 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 'LI' 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 > Now your problem is that the .pdb file is misformatted. Your residue name columns are shifted, such that pdb2gmx thinks "LI" is the residue and "G" is the chain identifier. PDB format is fixed; if you mess it up, the contents become unreadable (or severely misinterpreted). -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? 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