[Chimera-users] scan and minimization of dihedral angle

[Milo Westler]

Thanks. I tried using the easy method and it didn't work. Here is my script:

from chimera import runCommand as rc
rc("minimize")
rc("~select")
rc("rotation 1 @C2 at C3")
rc("rotation 1 90 1")
rc("select :@C1 at C2@C3 at C5")
rc("minimize freeze selected")



If I did the first command in a script, followed by a separate script using
the next 3 commands, then another separate script for the last 2, it
worked. If I have done something wrong, please tell me. Obviously, I could
write a bunch of scripts and run them separately, but I was trying to be
efficient. I want to do a potential energy scan with smaller angles (~10
degrees or so). I can write a script to write all of these separate scripts
and then run them in tandem, but that can be rather tiring.  I am also
interested in using chimera python scripts ( I promised myself I would
learn python).

I also sent a second message asking how to write out the parameters
determined from antechamber. (write prmtop doesn't work for me)


On Sun, Aug 24, 2014 at 1:32 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Milo,
> You can script most of it with Chimera commands:
>
> activate torsion (do that part just once), increment torsion with
> “rotation”:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
>
> select atoms to be frozen (or not) in minimization with “select":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
>
> “minimize” command:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
>
> That would still entail saving the Reply Log and editing it yourself.  For
> saving log contents, these previous posts may be useful:
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html
> >
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Aug 24, 2014, at 8:11 AM, Milo Westler <milo at nmrfam.wisc.edu> wrote:
>
> > Hi,
> >   I want to to a potential energy scan of a dihedral (of a small organic
> molecule) by setting a dihedral angle, fixing those atoms involved, and
> doing a minimization. Then incrementing the angle and repeating. I can
> currently do all of this by using the gui (set torsion angle in
> build_structure,minimize with selected atoms fixed , then save and edit the
> final energies for each angle in reply log). I'm sure that this can be done
> with python. I am wondering if there is an available script to do this
> all.  As input I would have a set of torsion angles and as output I would
> like a table of angle and energy.
> >
> > --
> > -- 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
> > =======================================================================
> ========
>
>


-- 
-- 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/20140824/277b6f3f/attachment.html>