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
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