Hi All;
Before asking query, please correct me if wrong...
I have positive vdwaal energy in amber output file so this mean more repulsion term is there. Thus less positive value means more stable compared to high positive value of vdwaal energy term.
I have two queries:
1) If I am studying two different ligands (one has polar atoms and other has more non-polar atoms) with same macromolecule (pocket being non-polar) in separate MD run having explicit solvent, Can I compare vdwaal energy directly from amber output file declaring contribution of vdwaal towards stability of complex? (less positive vdwaal energy more stable, less repulsion and more positive vdwaal less stable, means more repulsion)
2) I have read as more non-polar atoms (say of ligand) are there in environment of non-polar atoms (say pocket of macromolecule) then complex will be more stable. So considering this can it be concluded that less positive vdwaal, I am getting, (in case of non-polar ligand with non-polar pocket) is due to this fact? and also I am getting more positive value of vdwaal energy (in case of polar ligand with same non-polar macromolecule pocket).
thanks and regards;
JIom
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Received on Sat Jan 21 2012 - 03:00:02 PST
