AMBER Archive (2003)

Subject: Re: intra-perturbed group (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 07 2003 - 11:55:29 CST

On Fri, Mar 07, 2003, amber_at_heimdal.compchem.ucsf.edu 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 

-- 

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