[AMBER] Lambda Exchange

From: Jeff Wereszczynski <jwereszc.iit.edu>
Date: Tue, 7 Oct 2014 21:19:29 -0500

Hi AMBER Community,

I'd like to use PMEMD to perform Hamiltonian replica exchange alchemical
calculations to compute the absolute binding free energy of a small
molecule to a protein. I'm a little confused on the implementation
though. It looks like I need to create a separate prmtop file for each
lambda value and that I can't use the icfe option, is this correct? If so,
I have a few other questions:

1. It looks like the easiest way to modify the charges is with ParmEd. Is
there a way to select a range of atoms and scale the charges on all of them
by a factor? While I could set each of them explicitly, it would be much
easier to scale them all in one command.

2. Is it possible to use a softcore potential for the vdw term?

3. If I want to compute the work functions for going between windows for
an mbar analysis, do I need to post-proccess the results? Is there a way
to do it on the fly? It looks like the ifmbar parameter requires icfe
(which is incompatible with replica exchange).

Thanks for your help,

Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology
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Received on Tue Oct 07 2014 - 19:30:02 PDT
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