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 ======================================================================= ========
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
Thanks, I'll try it. On Thu, Aug 10, 2017 at 5:58 PM, Elaine Meng <meng@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@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@nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========
participants (2)
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Elaine Meng -
Milo Westler