[gmx-users] ionomer topolgy

[Ehsan Sadeghi]

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
-------------------------------------------------------

Thanks,
Ehsan

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, September 27, 2013 5:50:00 PM
Subject: Re: [gmx-users] ionomer topolgy



On 9/27/13 8:43 PM, Ehsan Sadeghi wrote:
> Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
>
> I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right?

Yes you did; you modified the Gromos96 53A6 force field.  There's nothing wrong 
with that; it's precisely what you wanted to do.  Also note that there is no 
such thing as a default force field.

> Here is the output from pdb2gmx. Thank you for your consideration.
>
> -----------------------------------
>
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading nafion3.pdb...
> WARNING: all CONECT records are ignored
> Read 46 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 2 chains and 0 blocks of water and 0 residues with 46 atoms
>
>    chain  #res #atoms
>    1 'G'     1     24
>    2 'H'     1     22
>
>
> WARNING: there were 1 atoms with zero occupancy and 45 atoms with
>           occupancy unequal to one (out of 46 atoms). Check your pdb file.
>
> 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.36#
> Processing chain 1 'G' (24 atoms, 1 residues)
> Warning: Starting residue LI0 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 'LI' 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
>

Now your problem is that the .pdb file is misformatted.  Your residue name 
columns are shifted, such that pdb2gmx thinks "LI" is the residue and "G" is the 
chain identifier.  PDB format is fixed; if you mess it up, the contents become 
unreadable (or severely misinterpreted).

-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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