On 10/25/13 11:32 AM, Sajad Ahrari wrote:
thanks for replying. are these features available under Gromacs? and is there
any tutorial or related material I can grasp to stand up for start?
My umbrella sampling tutorial covers generating a PMF. MM/PBSA is just a
post-processing technique, requiring software external to Gromacs. The MD
itself is no different and can be done with Gromacs.
-Justin
On Friday, October 25, 2013 6:46 PM, Justin Lemkul <[email protected]> wrote:
On 10/25/13 11:07 AM, Sajad Ahrari wrote:
> Hello dears
> searching through literature, many cases of LIE method application for BFE
calculation of small molecules are on hand . but I couldn't find any report of
using this method for interaction of small peptides and proteins. I wanted to
know if the protocol prepared in Justin tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html)
can be used in such case? and if so, should I apply any constrain on rotatable
bonds of peptide along the simulation within the non-bonded state?
PMF or MM/PBSA calculations are far better suited for studying these types of
interactions.
-Justin
--
==================================================
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
[email protected] <mailto:[email protected]> |
(410) 706-7441
==================================================
--
==================================================
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
[email protected] | (410) 706-7441
==================================================
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