[Chimera-users] scan and minimization of dihedral angle

Milo Westler milo at nmrfam.wisc.edu
Thu Aug 28 13:46:18 PDT 2014

Thanks for your help. I got it to run ok. I was a bit taken back by the
numbers until I discovered the energy is in KJ/mol. I'm not sure if anyone
is interested but, I have attached 2 perl scripts (sorry, I don't know
python) that generates the python script for chimera then analyzes the

Make PE_scan.pl (pot_energy.pl) and executable and type PE_scan.pl (and
pot_energy.pl)  for instructions.

One requirement is that the atoms (involved in the dihedral angle) must
have unique names in the structure file.

~>PE_scan.pl C1 C2 C3 C4 > PEscan.py

open your molecule in chimera and on the command line type:  open PEscan.py

An output file is generated named: reply_log.txt

An angle (degrees) vs. energy (kJ/mole) table is produced upon running

~>pot_energy.pl reply_log.txt >energy

If you have xmgrace installed:

~>xmgrace energy

will plot it.

Hopefully I have caught all of the bugs, but one never knows.

On Tue, Aug 26, 2014 at 1:51 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On Aug 26, 2014, at 11:49 AM, Eric Pettersen <pett at cgl.ucsf.EDU> wrote:
> dihed = angle(":241,a at CA,CB,CG,ND")
> Not that it matter too much, but I meant :241.a, not :241,a in the example.
> --Eric

-- Milo
National Magnetic Resonance Facility at Madison
      An NIH-Supported Resource Center

W. Milo Westler, Ph.D.

NMRFAM Director
Senior Scientist
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
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