Re: [AMBER] Amntechamber MOPAC and SQM

From: David A Case <case.biomaps.rutgers.edu>
Date: Sat, 15 Feb 2014 10:33:56 -0500

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
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