[gmx-users] Creating custom position restraints for a multi-chain protein

[Kolmus, Elizabeth K.]

Are there any plans to address this in future releases? I realize you already have enough work on your plate to last you for years, but I can't be the only person wanting to treat some portions of a multimeric molecule differently than others.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, June 30, 2015 5:35 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Creating custom position restraints for a multi-chain protein

On 6/30/15 5:20 PM, Kolmus, Elizabeth K. wrote:
> Hello,
>
>
> I am attempting to create my own set of position restraints for a protein with 4 chains. However, this fails when I attempt to run the files through grompp. Here is the workflow:
>
>
> gmx make_ndx -f protein.pdb -o chain-n.ndx (for n = 1-4)
>
>      del 0-9
>
>      r x-y | r z-w & chain n
>
>      name 0 ChainN
>
>      q
>
>
> gmx genrestr -f protein.pdb -n chain-n.ndx -o posre_Protein_chain_N.itp
>
>
> When I take the resulting .itp files and try to pre-process with them, I get the following error:
>
> Program gmx, VERSION 5.0.5
> Source code file: /usr/local/gromacs-5.0.5/src/gromacs/gmxpreprocess/toppush.c, line: 1806
>
> Fatal error:
> [ file posre_Protein_chain_B.itp, line 699 ]:
> Atom index (6413) in position_restraints out of bounds (1-6412).
> This probably means that you have inserted topology section "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
>
>
> The issue is not actually with where the section is placed. It is placed in the correct file - topol_Protein_chain_B.itp . However, topol_Protein_chain_B.itp numbers atoms from 1-6412, and posre_Protein_chain_B.itp begins at atom 5512, as per the protein.pdb atom numbering. How can I renumber the atoms in posre_Protein_chain_B.itp (and the other two files) in an intelligent way?
>

Restraints only work on per-moleculetype numbering.  Please note the WARNING in
the genrestr help information.

The only way to get the desired outcome is to process individual coordinate
files of each chain, separately.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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