Re: intra-perturbed group (fwd)

From: David A. Case <>
Date: Fri, 7 Mar 2003 09:55:29 -0800

On Fri, Mar 07, 2003, wrote:
> For free energy calculations using INTPRT=5, how does amber find the
> intra-perturbed group within a molecule.
> I think that it looks for atom types, bond lengths, angles, and torsional
> parameters that are changing from the initial to final state in FEP, but I a
> not sure. What about non-bonded and 1-4's. Do these go into deciding
> whether an atom is within the intra-pert group or not. Basically my
> question is what criteria does amber use to decide if an atom is part of
> the intra-pert group or not for the INTPRT calculations.

I'm pretty sure that if all of atoms involved in a force field term are
changing, that term is considered to be "intrapertubed"; it doesn't matter
what kind of term it is (i.e. bond, angle, 14, nb). It is not an atom that
is "part of the intra-pert group", but rather a term in the force field that
does (or does not) fall into this category.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Fri Mar 07 2003 - 18:53:01 PST
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