This is straightforward when post processing a trajectory. Look in the
idecomp flag. you need a recent amber version, and you didn't specify wht
you have.
On Jul 19, 2012 5:48 PM, "Fabrício Bracht" <bracht.iq.ufrj.br> wrote:
> 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 - 16:30:02 PDT
