AMBER Archive (2009)

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

From: Alan (
Date: Thu Jun 04 2009 - 09:19:28 CDT

Thanks David,
But I still want to understand better this "Antechamber actually computes a
minimized structure" assertion because I would like to know why I got this
msg sometimes when running antechamber:

Warning: Close contact of 1.932973 angstroms between .R<MOL 1>.A<C7 8> and
.R<MOL 1>.A<H1 21>

I got this warning after 'minimisation'? I definitely would like to find a
way of calculating myself QM/semi-empirical minimisation. As you mentioned,
I will try to find how to do it with mopac explicitly.


On Tue, May 26, 2009 at 12:41, David A. Case <>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
> _______________________________________________
> AMBER mailing list

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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