AMBER Archive (2009)

Subject: Re: [AMBER] ligand QM/semi-empirical coords optmisation

From: Junmei Wang (junmwang_at_gmail.com)
Date: Fri Jun 05 2009 - 10:01:32 CDT

Antechamber does perform AM1 optimization when generates the bcc charges.
The output structure is the original structure while charges are based upon
the AM1-optimized structure. The AM1-optimized structure is written out in
mopac.pdb in the current directory.

It is a good idea to add an option to use the optimized structures. We will
add this option in the later versions

Best

Junmei

On Tue, May 26, 2009 at 6:41 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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
> calculation.
>
> ...dac
>
>
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