AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu May 13 2004 - 13:41:18 CDT

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)
>
> ANTECHAMBER_MUL.OUT
> ...
> ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
> 1 P -1.0000 6.0000
> 2 O -.3932 6.3932
> 3 O -.3678 6.3678
> 4 O .6808 5.3192
> 5 P 2.6773 2.3227
> 6 O -1.2583 7.2583
> 7 O -1.2465 7.2465
> 8 O -1.2695 7.2695

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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