Dear Amber team,
I have a general question regarding consistency of the Amber FF protocols in
the context of free energy calculations.
If a simulation is using AMBER99 + GAFF + AM1BCC charges then we should use
a GAFF minimised geometry for the ligand.
If a simulation is using AMBER99 + GAFF + RESP charges then we should use a
GAFF minimised geometry for the ligand, and not the geometry obtained via QM
when doing resp to be consistent with the protocol.
Any issues on that?
Thank you very much
Aiko
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Received on Tue Mar 16 2010 - 07:00:03 PDT
