Hi all,
> I am pretty sure that there is no way to do FEP calculations in amber at
> this moment.
there is a way to collect the necessary energy values for FEP evaluation
using the bar-module (see section 4.1.3 of the Amber11 manual) which is
geared to produce data usable with Michael Shirts pyMBAR-scripts. It is
not very well used, maybe because the Amber community is more used to TI
calculations. Also, it does not support softcore-potentials (yet) which
may be needed depending on the system.
So if you really want to do FEP and not TI for your free energy
calculation, it is possible, but be sure this is what you really want. It
would be best if you are familiar with doing TI calculations in Amber
first, which are much better documented.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Oct 10 2011 - 02:00:02 PDT
