AMBER Archive (2009)

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

From: Alan (
Date: Tue May 26 2009 - 05:55:09 CDT

Hi there,
I was wondering if there's a reasonable good method to improve the coords of
ligands. I took a look at RED using gamess to try to optmise the structure
of a ligand, but as RED devs reports, this may fail and indeed failed for

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.

We have a small DB here in which it was used Corina, but frankly, I don't
like much this approach and I would like to compare these results with
something that would be more soundly meaningful for me.

Many thanks in advance.


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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