[gmx-users] pdb2gmx and periodic molecule

Justin Lemkul jalemkul at vt.edu
Sat Apr 25 15:15:24 CEST 2015

On 4/25/15 12:00 AM, Alex wrote:
> Ahoy,
> What I have here is a 100% precisely set up periodic ssdna chain of
> six residues without termini. The goal is to get the 'polymerization'
> across the box. So, I boxed the chain and set up the periodicity pretty much
> perfectly.
> To test, translation in the direction of periodicity by the
> periodicity constant results in bonds perfectly recognized by things like VMD or
> pymol (in the concatenated structure).
> When running pdb2gmx on the boxed structure, the periodicity seems to
> be ignored and then expectedly I get a fatal error with a custom FF that works
> fine on finite chains.
> x2top sees pbc, but we're not using it here. So, no topology in sight.
> Any ideas?

pdb2gmx isn't designed to intuitively handle such cases.  The best way to go 
about it is:

1. Run pdb2gmx normally to add H that you might need and to apply patching such 
that you have a phosphate on one end and an alcohol on the other (presumably you 
already have this last part done and have suitable .tdb entries).

2. Delete unnecessary atoms from the termini.

3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't 
complain at you about dangling termini.

4. Manually edit the topology to introduce the needed bond, angles, and dihedrals.



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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