[gmx-users] Lie method for binding free energy calculations

Justin Lemkul jalemkul at vt.edu
Fri Oct 25 17:16:57 CEST 2013

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 



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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