[gmx-users] How to get an infinite DNA topology

[Justin Lemkul]

On 6/1/16 11:40 AM, elixer at mail.ustc.edu.cn wrote:
> Hello everyone, I am working on a MD simulation using AMBER99 force field
> with gromacs in a system including a very long A-type DNA fragment. My plan
> is to build a cell containing exact 11 DNA base bair (which is a circle of
> A-type DNA), and with periodic boundary conditions to get an infinite DNA
> topology. But the problem is that pdb2gmx reports a fatal error: Atom P in
> residue DA 2 (which is my first DNA residue from 5' end) was not found in rtp
> entry DA5 with 30 atoms while sorting atoms. It looks like the program is
> trying to find the residue of 5' end in a DNA fragment with limitid length,
> which is not existed in my system. The 5' end DNA residue is a little
> different from a normal DNA residue, like it is short of a P atom, which is
> probably why the error occurs. So is there a way to prevent the program from
> trying to find the 5' end DNA fragment? Or is there any other way to build an
> infinite DNA topology? Best regards, Elixer
>

This is happening because AMBER force fields use terminal specific residues 
rather than normal .tdb entries.  The way to hack around this is to comment out 
the renaming columns in dna.r2b in the force field directory.  To get pdb2gmx to 
finish, you'll probably also have to use -missing and edit the topology 
accordingly to include the bonded interactions that will be formed across PBC. 
Then use "periodic_molecules = yes" in any .mdp file.

-Justin

-- 
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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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