I would like to define a new residue, e. g. a small molecule or ion, within Amber using the amoeba force field. I can see how to add to the amoebapro.prm file the various amoeba-like parameters that I would determine by fitting to ab initio calculations. But it is not clear how to define a residue that will make use of these new parameters. How can this be done? Is there an example somewhere?
Dan Chipman
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# Daniel M. Chipman
# Radiation Laboratory
# University of Notre Dame
# Notre Dame, IN 46556
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Received on Wed Mar 30 2011 - 13:00:07 PDT
