Thanks a lot. I understood it completely now
Nitin Sharma
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Saturday, February 15, 2014 11:34 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Amntechamber MOPAC and SQM
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 - 08:30:03 PST
