AMBER Archive (2008)

Subject: Re: AMBER: problem with antechamber

From: Junmei Wang (
Date: Thu Feb 28 2008 - 09:06:31 CST

Antechamebr is developed to handle organic molecules. It does can handle
some inorganic molecules, but not all. For your molecule, you may try "-j
5" flag when running antechamber.



On Wed, Feb 27, 2008 at 11:55 PM, aneesh cna <> wrote:

> Respected Users
> I am using version 9.0 of Amber .
> I did the gaussian calculation for a charged molecule PF6, to find its ESp
> charges. While generating the prepi file using the Antechamber module in
> Amber I got the following error:
> For atom[1]:P1, the best APS is not zero, exit
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time
> What is the reason for such error?
> I tried checking the gaussian output file but the structure obtained from
> the gaussian is looking fine
> Expecting an early reply
> Thanks
> Aneesh

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