AMBER Archive (2009)
Subject: Re: [AMBER] ligand QM/semi-empirical coords optmisation
From: Alan (alanwilter_at_gmail.com)
Date: Thu Jun 04 2009 - 13:05:27 CDT
You're right, it's from Leap, but I mixed things because now in Sleap,
'antechamber' is called automatically (set default fastbld on).
Anyway, I maybe still need something more robust. It's because I have a DB
with almost 9000 ligands and acpypi/antechamber/mopac worked for ~75%, but I
have several inputs there that doesn't have a good initial structure or
Corina didn't do a good job.
On Thu, Jun 4, 2009 at 16:06, David A. Case <case_at_biomaps.rutgers.edu>wrote:
> On Thu, Jun 04, 2009, Alan wrote:
> > But I still want to understand better this "Antechamber actually computes
> > minimized structure" assertion because I would like to know why I got
> > msg sometimes when running antechamber:
> > Warning: Close contact of 1.932973 angstroms between .R<MOL 1>.A<C7 8>
> > .R<MOL 1>.A<H1 21>
> > I got this warning after 'minimisation'? I definitely would like to find
> > way of calculating myself QM/semi-empirical minimisation. As you
> > 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.
> 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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