[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)

[Justin Lemkul]

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.

-Justin

>
> 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,
>> Gaurav
>> School of Biochemical Engineering.
>> Indian Insitute of Technology (BHU), Varanasi.
>> India.
>>
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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

==================================================