[Chimera-users] scan and minimization of dihedral angle

Elaine Meng meng at cgl.ucsf.edu
Sun Aug 24 11:32:39 PDT 2014


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
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> Madison, WI USA 53706-1544
> EMAIL: milo at nmrfam.wisc.edu
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