Many thanks Justin. Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling.
I also have some concern about my pdb file. i generated from my drawing in Avogadro, with some arbitrary bond length and angle. I hope that I can find the correct bond length and angle with energy minimization; am, I right? Kind regards, Ehsan ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Monday, September 30, 2013 11:27:25 AM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 2:23 PM, Ehsan Sadeghi wrote: > Yes, I have introduced the new .rtp entry in > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. > What could be wrong? > The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would not throw that error. Can you provide the output of: grep LIG /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -Justin > > ----- 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
