[gmx-users] Regarding siRNA simulation.

[Justin Lemkul]

On 9/28/14 7:36 AM, Anurag Dobhal wrote:
> I am simulating an RNA molecule in which  first residue has a 5'-PO4 cap,
> which is uncommon. I am adding the atoms and bond parameters in the .rtp
> files in the existing force field directories but these parameters are not
> getting saved. I am using Amber 99 force field and i am making changes in
> the rna.rtp file.
>
> How can i make these changes possible.
> Do I need to write new .rtp file.
>

No, you need a suitable .tdb entry that specifies a phosphate instead of a 5'-OH 
group.  You could, in theory, create a special residue in the .rtp file, but a 
.tdb entry is much simpler and eliminates the need to create a special residue 
name, residuetypes.dat entry, etc.

-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 601
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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