AMBER Archive (2009)

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

From: David A. Case (
Date: Thu Jun 04 2009 - 10:06:28 CDT

On Thu, Jun 04, 2009, Alan wrote:

> 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.

As I said earlier, antechamber uses the AM1-minimized structure to get
the am1-bcc charges, but then discards that, and uses the original input
coordinates in the output mol2 or prepin files. The message you quote
above looks like it comes from LEaP, not from antechamber.

I've often thought that we should have an option to output
the minimized structure -- I'll cc this to junmei for comment.


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