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

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