AMBER Archive (2008)

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

From: David A. Case (
Date: Mon Jun 02 2008 - 19:12:55 CDT

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)