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
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center

W. Milo Westler, Ph.D.

NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive
Rm B160D
Madison, WI USA 53706-1544
EMAIL: milo@nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
======================================================================= ========