AMBER Archive (2003)

Subject: intra-perturbed group (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Fri Mar 07 2003 - 11:13:57 CST

---------- Forwarded message ----------
Date: Thu, 6 Mar 2003 16:29:26 -0400
From: Sophia Kondratova <x357l_at_unb.ca>
To: amber <amber_at_heimdal.compchem.ucsf.edu>
Subject: intra-perturbed group

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.

Thanks in advance for any help.

Sophia Kondratova