[gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

[Peter Stern]

Even though it's called aminoacids.n.tdb?  Or a different name, e.g. nucleicacids.n.tdb?
One problem is that I eventually have to deal with tens, maybe hundreds of complexes.  
Some, of course, will have the normal 5' nucleotide.  Will I be able to choose the appropriate n.tdb file for each case
or will I have to copy the appropriate one to my run directory each time?  I guess the latter. 

Thanks,
Peter

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Monday, June 22, 2015 9:39 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'



On 6/22/15 2:36 PM, Peter Stern wrote:
> I have a chain of RNA in complex with a protein.
> The pdb file is missing the first two nucleotides and starts with the third including the PO2 group.
> pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the topology from rna.rtp using RA5 as the "residue" type.
> Thus it  doesn't like the fact that the coordinates contain a P atom and fails.  I would like to avoid removing the coordinates for PO2.
> How can I get pdb2gmx to treat the first (and last in other cases) nucleotide as a "normal" residue?
> Simply changing the name of the residue from A to RA does not work.
>

You'll need to create an entry in the .n.tdb file that specifies a 5'-phosphate cap.

-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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