Re: AMBER: Antechamber: problems with bcc correction

From: David A. Case <>
Date: Sun, 25 Apr 2004 00:26:59 -0700

On Fri, Apr 23, 2004, Oliver Hucke wrote:
> I am using antechamber to prepare my ligands.
> One rather complex ligand contains a pyridine moiety.
> After calculation of the partial charges (amber8 antechamber with the
> AM1BCC method and divcon) I noticed a very small negative charge of the
> nitrogen (-0.131).
> I repeated the calculation for the pyridine molecule. The nitrogen
> charge was calculated as -0.1385.
> The same input structure used with an older version of antechamber and
> mopac gave -0.6645 !

The problem seems to be in using a mol2 file as _input_ to antechamber. If I
convert the mol2 file to a pdb file (antechamber does this part OK), then I
get -0.6646 with the Amber 8 version of antechamber, essentially the same
value as we both get for Amber 7.

Until we sort this out, users should not use the mol2 format to get input
into antechamber. Junmei Wang, the author of antechamber, reads this list,
and I am sure that he will work on this as quickly as he can, and I will
look at it as well.

Thanks for the report. I hope this will fix your problem. regards...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Sun Apr 25 2004 - 08:53:00 PDT
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