AMBER Archive (2002)

Subject: Gibbs (FEP) (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Mon Aug 26 2002 - 16:50:36 CDT

---------- Forwarded message ----------
Date: Thu, 22 Aug 2002 14:29:11 +0000
From: sara nunez <mbdtssn_at_hotmail.com>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Gibbs (FEP)

Hello everyone,

I'm trying to compute the activation free energy (using FEP in Gibbs module)
of a proton transfer reaction of an enzyme.

I have tried to load the reactant of the reaction (state 0) and the
Transition State of the reaction (state 0) in leap. I also modified the
charges and parameters for the state 0. But when I tried to save the parm
and coord files of the perturbed state 1(saveAmberParmPert), leap complained
that I was missing some bonds, angles and dihedral parameters concerned with
dummy atoms.

Can anyone tell me how to create the dummy atoms parameters in order to
do this?

Many thanks

sara

Sara Nunez
Theoretical & Computational Chemistry Group
University of Manchester
Manchester, M13 9PL
United Kingdom

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