Hi Milo,
In your command script, include the “addh” and “addcharge” commands (with whatever options you want) before the “minimize” command, instead of having the minimization call these steps.   You want the addcharge option “method gas”, see:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 10, 2017, at 1:35 PM, Milo Westler <milo@nmrfam.wisc.edu> wrote:
>
> We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method?
>
> Currently we use:
> chimera --nogui --silent R.mol opt.cmd
>
> Where opt.cmd is:
> minimize
> write #0 R_min.pdb
>
> --
> -- Milo