[Chimera-users] command line minimization
milo at nmrfam.wisc.edu
Wed Aug 16 06:32:33 PDT 2017
Thanks, I'll try it.
On Thu, Aug 10, 2017 at 5:58 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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:
> I hope this helps,
> 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 at 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
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
Department of Biochemistry
University of Wisconsin-Madison
DeLuca Biochemistry Laboratories
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo at nmrfam.wisc.edu
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