[gmx-users] ionomer topolgy
esa38 at sfu.ca
Mon Sep 30 22:40:27 CEST 2013
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?
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at 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
> ----- Original Message -----
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "Discussion list for GROMACS users" <gmx-users at 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 A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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