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

Kolmus, Elizabeth K. kolmusek at ornl.gov
Wed Jul 1 16:09:10 CEST 2015

Here's the solution I came up with, for posterity.

My protein has four chains, two of each type. I left the first chain alone, since gromacs handles it just fine, but pulled out the second chain into its own PDB and renumbered the atoms:

gmx make_ndx -f protein.pdb -o chain-b.ndx
    del 0-9
    chain b
gmx editconf -f protein.pdb -n chain-b.ndx -o chain-b1.pdb 
gmx genconf -f chain-b1.pdb -o chain-b.pdb -renumber

This can be done as many times as needed for as many types of chains as there are.

I then created indices for the parts of the protein I wanted restrained:

gmx make_ndx -f protein.pdb -o struc-a.ndx
    del 0-9 
    r x-y | r z-w | ... | r n-m & chain a [SEE NOTE BELOW] 
    name 0 StructureA      

gmx make_ndx -f chain-b.pdb -o struc-b.ndx
    del 0-9 
    r a-b | r c-d | ... | r i-j 
    name 0 StructureB

Again, this can be done more than twice if needed. If the residue numbering in your PDB file doesn't start over at 1 for each chain, you can leave off the "& chain x" part.

Finally, I generated the restraints, and made copies using the command line (BACK UP THE ORIGINAL POSRE ITP FILES, JUST IN CASE):

gmx genrestr -f protein.pdb -n struc-a.ndx -o posre_Protein_chain_A.itp
gmx genrestr -f chain-b.pdb -n struc-b.ndx -o posre_Protein_chain_B.itp
cp posre_Protein_chain_A.itp posre_Protein_chain_C.itp
cp posre_Protein_chain_B.itp posre_Protein_chain_D.itp

You don't need to make copies if you don't have symmetrical units in your protein.

I hope this helps others who run into a similar issue with renumbering atoms in .itp files. 
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 6:01 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Creating custom position restraints for a multi-chain protein

On 6/30/15 5:42 PM, Kolmus, Elizabeth K. wrote:
> 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.

Anyone is welcome to submit a feature request on redmine.gromacs.org (or even
better, help write the code!) but this would remain a very low priority for the
dev team unless someone is really enthusiastic about it.  The tool is stated to
be pretty much a uni-tasker, and there are several workarounds for multimeric
systems (modify the .itp files that pdb2mgx writes, separate the coordinates and
process them individually, clever use of awk, etc).



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

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