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?
best,
Sajad
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