[gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

[Justin Lemkul]

On 11/18/13 8:26 AM, Tomek Wlodarski wrote:
> Hi,
>
> I would like to run simulation of short peptide (nascent chain) bound to
> tRNA (in amber ff).
> Do gromacs supports chains which have both protein and nucleic acid
> components?
> I have problem with termini of this chain:
> gromacs is trying to find 3'- terminus of RNA - but it can't because
> terminus of the chain is amino acid type...
> I know that I have to parametrize bond between nucleotide and protein.
> Should I change type of this chain to either RNA or protein - e.g. by
> creating special class in aminoacid.rtp which includes nucleotides (with
> new names)?

You'll probably have to write the protein and RNA as separate chains in the 
input coordinate file, then use specbond.dat to assign the bond in conjunction 
with pdb2gmx -chainsep and/or -merge.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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

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