[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)
jalemkul at vt.edu
Fri Mar 28 14:54:36 CET 2014
On 3/28/14, 9:46 AM, chetan kumar meena wrote:
> try prodrug for small molecule for topology generation.
PRODRG produces unreliable topologies. Greater care needs to be taken to
parametrize nonstandard amino acids and other compounds.
> On Fri, Mar 28, 2014 at 3:03 PM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT
> (BHU) <gaurav.saraf.bce09 at itbhu.ac.in> wrote:
>> Respected Sir/Ma'am
>> I am new to the field of simulations and want to perform
>> protein-peptide simulations. I am facing troubles with building the
>> topology for my peptides as they contain various modified amino acids
>> which the rtp does not recognise.
>> Attachments: one of the pdb file of a lantibiotic (2KTO is the RCSB code)
>> Thanking you,
>> Yours sincerely,
>> School of Biochemical Engineering.
>> Indian Insitute of Technology (BHU), Varanasi.
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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
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