Minhazul,
The standard route to umbrella sampling simulations (as outlined in the
AMBER manual) is to use the nmropt module. A variety of coordinates and
harmonic-like potential forms are available and can be specified in an
additional restraint file (which is referenced in mdin).
Regards,
Brian
On Sat, Jan 12, 2013 at 11:07 AM, minhazul arfeen
<minhazularfeen.gmail.com>wrote:
> Dear Sir,
>
>
> I wish to perform Molecular dynamics simulation using umbrella sampling for
> my target protein-ligand complex, But i am not able to get, how to define
> path and direction of reaction coordinates in the mdin files for the
> simulation runs.
>
> Thanks in advance.
>
> --
> Warm Regards
>
> Minhazul Arfeen
> Ph.D. Scholar
> Department of Medicinal Chemistry.
> National Institute of Pharmaceutical Education And Research.
> Mohali
>
>
>
> --
> Warm Regards
>
> Minhazul Arfeen
> Ph.D. Scholar
> Department of Medicinal Chemistry.
> National Institute of Pharmaceutical Education And Research.
> Mohali
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Sun Jan 13 2013 - 10:00:03 PST
