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

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