Hello. If one had a molecular dynamics simulation of a solvated
protein (in this case, water is the solvent), and was interested in
retrieving VdW and Coulomb interaction energies between pairs of
residues (very specific pairs of residues. Just in case you are
wondering, there are no ligands, just protein residues) for this
particular simulation. What would be the best way to do this in Amber?
The idea here is see the effect that a mutated residue has in one(or
more) of the catalytic site residues.
Thank you
Fabrício Bracht
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Received on Thu Jul 19 2012 - 15:00:02 PDT
