Re: The accuracy of FEP calculation

From: Chris Chipot (
Date: Thu Feb 11 2010 - 10:45:18 CST

Dear Mary,

there is of course a need to include positional restraints as the
ion is being grown in protein, because at λ = 0, when the two do
not interact, the former is free to move astray far from the binding
site. Positional restraints can be enforced, for instance, using the
keyword extraBonds in NAMD or the Colvars module. Be aware, however,
that enforcing such restraints is tantamount to a loss of translational
entropy, which, accordingly, ought to be measured in terms of free
energy. Luckily, in the case of an ion, this quantity can be evaluated
analytically rather easily. This problem is being dealt with in the
new version of the FEP tutorial, which is either already out, or will
be so very shortly.

Chris a écrit :
> Hi all,
> I am using FEP to calculate the binding energy of Na ion inside the
> protein. I did not put any restraint on the ion and observed that later on
> this ion moved away from the binding site. This ion is supposed to
> disappear finally. Should ion's moving away from the binding site affect
> the binding energy? I think I may need to restrain it. Any suggestion?
> Thanks,
> Mary

Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
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