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

[Mark Abraham]

Hi,

On Mon, Jun 22, 2015 at 8:50 PM Peter Stern <peter.stern at weizmann.ac.il>
wrote:

> 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.
>

As you will see when you look at e.g the example in the charmm27.ff folder,
that file is a database of things that might match to the first residue. So
if there's a phosphate cap that'll get used. Or a normal nucleotide will
match normally.

Mark


> 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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