I've checked the AmberTools manual for the ptraj action command "closest".
My question is whether there is a distance cutoff between the residues specified in the mask and the first atom in the solvent molecule.
A related question is whether there is a way to work out the -per frame - number of solvent molecules buried in the binding site of a receptor/ligand complex in the course of trajectory.
Thanks in advance for any advice
Regards
George
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Received on Thu Jan 12 2012 - 10:00:03 PST
