AMBER Archive (2004)

Subject: Re: AMBER: antechamber/Mopac: strange GTP charges

From: Raik Grünberg (
Date: Fri May 14 2004 - 05:35:13 CDT

Hi Heather, Hi David,

thanks for your fast response! I'll wait for the GTP parameters that Heather
kindly offered. Nevertheless, in order to learn something here, it would
still be nice to know what went wrong. I've put my mopac input and output on
the web

The energy appears to converge well but then there is a strange jump in the
last few cycles and the program declares convergence even though it doesn't
look like that at all.

I've also put up the mopac7 executable - it runs on our redhat 7.3 systems
(the provided test case works) although it was compiled on 6.2 (again the
merit goes to Tru, our sysadmin). Perhaps, it is useful for others as well.
Or perhaps there is a general problem with this mopac version?

Best regards

On Thursday 13 May 2004 20:41, David A. Case wrote:
> On Thu, May 13, 2004, Raik Grnberg wrote:
> > I generated parameters for GTP with:
> >
> > antechamber -i GTP_in.pdb -fi pdb -o GTP_bcc.prep -fo prepi -nc -4 \
> > -rn GTP -at amber -c bcc
> >
> > Thanks to our sysadmin (who spend a day to compile mopac7 on a (virtual)
> > redhat 6.2 machine) I could now use the mopac charges - technically
> > everything looks fine. But unfortunately the charges don't really make
> > sense (not to me at least). Furthermore the charges are very different
> > between the mopac output and the prep / pdb.
> > Have a look at the phosphates (equivalent atoms get different charges,
> > oxygen with positive charge, P with -1.0000)
> This does look wrong. You should carefully examine the mopac output to see
> if it reached a good minimum, if the heat of formation and geometry are
> reasonable, etc. (My personal experience with mopac7 has never been very
> good, in the sense that calculations could appear to converge, but still
> give bad answers. But of course, this does not mean that it is the
> program's fault here.)
> ...regards...dac
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