I'm happy you got things to work. Thanks for sharing the scripts! --Eric On Aug 28, 2014, at 1:46 PM, Milo Westler <milo@nmrfam.wisc.edu> wrote:
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 output.
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.
~>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@cgl.ucsf.edu> wrote: On Aug 26, 2014, at 11:49 AM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
dihed = angle(":241,a@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 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 ======================================================================= ======== <PE_scan.pl><pot_energy.pl>