[gmx-users] ionomer topolgy

[Ehsan Sadeghi]

Hello,

When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are misplaced. I am using Avogadro for building the atomistic structure, it uses "connect" command to connect atom correctly. After running pdb2gmx, the generated files do not have "connect" and they put the bonds is some random places. An suggestion for solving this problem or any other software for building structure without having this problem?

If I just want to consider bond stretching in my analysis, what should I do to tell gromacs neglect angle,improper, and dihedral? I received 89 errors for not defining them.

Kind regards,
Ehsan

----- 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

-Justin

>
> ----- 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
>

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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