AMBER Archive (2008)

Subject: Re: AMBER: gasteiger is not working with ambertools 1.0

From: Alan (alanwilter_at_gmail.com)
Date: Tue Jun 03 2008 - 09:44:07 CDT

Thanks David, that solved the issue.
Cheers,
Alan

On Tue, Jun 3, 2008 at 1:12 AM, David A. Case <case_at_scripps.edu> wrote:

> On Mon, May 19, 2008, Alan wrote:
> >
> > antechamber -i dmp.pdb -fi pdb -o dmp_gas_sybyl.mol2 -fo mol2 -c gas
> > -s 2 -df 0 -at sybyl
> >
> > Error message: The net charge of the molecule (-9999) does not equal
> > to the total charge (0.00 ) based on Gasteiger atom type, exit
> >
> > is simply not working anymore. It was working pretty fine with
> antechamber
> > 1.27.
> >
>
> antechamber now seems(?) to require the user to specify the net charge (via
> the -nc option) when computing gasteiger charges. It doesn't (any longer?)
> default to zero. (This is based on a quick read of the sources.)
>
> So, try adding '-nc 0' to your command line and see if that helps.
>
> ...good luck...dac
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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