[Chimera-users] command line minimization

Milo Westler 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:
>
> <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 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
>
>


-- 
-- 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 at nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
=======================================================================
========
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170816/415575c3/attachment-0001.html>


More information about the Chimera-users mailing list