On Sat, Feb 15, 2014, Nitin Sharma wrote:
>
> will there be a significant difference in binding free energy results on
> using ligand.mol2 instead of sqm.pdb if the original pose of the ligand
> was generated as a result of docking.
I guess you would have to run an experiment to find out. If you have a
docking pose, then using a minimized structure (as in sqm.pdb) would be
somewhat involved--you would have to re-dock the molecule back into the
binding site. This is the reason that most people discard the information
in sqm.pdb.
...dac
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Received on Sat Feb 15 2014 - 08:00:03 PST
