AMBER Archive (2006)

Subject: Re: AMBER: Mutual exclusion of atoms

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Nov 06 2006 - 16:02:47 CST

Dear Nitin,

> I have to build a system where I want that a set of atoms should not
> "see" atoms from another set ie., they should be mutually excluded. I

as far as I know (which might not be very far), amber does not have this
capability. But with the free energy perturbation facilities as they are,
a change from one molecule to another can be accomplished. You would
set up a prmtop file for both your starting and ending states and
simulate the transition between them. In this way the 'old' and 'new'
molecules do not per se interact with each other, rather you have
simulations of mixed states that have partially characteristics of one
molecule and partially of the other.

The amber9 manual p153+ explains how that is done. Be careful, if your
molecules are very different, the amount of sampling necessary to obtain a
converged transition might be huge.

If the two compounds to compare are very different in number and types of
atoms etc., you might need to set up your transformation as two separate
steps. Find out the largest common scaffold of your two molecules and
prepare thermodynamic integration calculations that change both the
molecules you want to compare into it. Simulate these two transitions and
sum up their results for the total dG of your two molecules.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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