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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
