AMBER Archive (2009)
Subject: Re: [AMBER] ligand QM/semi-empirical coords optmisation
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue May 26 2009 - 06:41:25 CDT
On Tue, May 26, 2009, Alan wrote:
> I don't need anything sophisticate so I was wondering if even mopac via
> antechamber would have a way of given a pdb of ligand try to improve its
> coordinates (and then I would do single-point charges with RED/gamess)
> either by QM or semi-empirical methods.
This sounds reasonable to me. Antechamber actually computes a minimized
structure when computing am1-bcc charges, but it doesn't save it anywhere.
But you could run the same mopac geometry optimization yourself. Of course,
how accurate you need the geometry to be will help determine whether
semiempirical QM is good enough, or whether you need a more accurate
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