<div dir="ltr"><div><div>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.<br>
<br></div>Make PE_scan.pl (<a href="http://pot_energy.pl">pot_energy.pl</a>) and executable and type PE_scan.pl (and <a href="http://pot_energy.pl">pot_energy.pl</a>) for instructions.<br></div><div><br>One requirement is that the atoms (involved in the dihedral angle) must have unique names in the structure file. <br>
</div><div class="gmail_extra"><br><br>~>PE_scan.pl C1 C2 C3 C4 > PEscan.py<br><br></div><div class="gmail_extra">open your molecule in chimera and on the command line type: open PEscan.py<br><br>An output file is generated named: reply_log.txt<br>
</div><div class="gmail_extra"><br></div><div class="gmail_extra">An angle (degrees) vs. energy (kJ/mole) table is produced upon running <a href="http://pot_energy.pl">pot_energy.pl</a>. <br><br>~><a href="http://pot_energy.pl">pot_energy.pl</a> reply_log.txt >energy<br>
</div><div class="gmail_extra"><br>If you have xmgrace installed:<br></div><div class="gmail_extra"><br>~>xmgrace energy <br><br>will plot it.<br><br></div><div class="gmail_extra">Hopefully I have caught all of the bugs, but one never knows.<br>
</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Aug 26, 2014 at 1:51 PM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word"><div class=""><div><div>On Aug 26, 2014, at 11:49 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.EDU" target="_blank">pett@cgl.ucsf.EDU</a>> wrote:</div>
<br><blockquote type="cite"><div style="font-family:Helvetica;font-size:medium;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
dihed = angle(":241,a@CA,CB,CG,ND")</div></blockquote><br></div></div><div>Not that it matter too much, but I meant :241.a, not :241,a in the example.</div><span class=""><font color="#888888"><div><br></div><div>
--Eric</div><div><br></div><div><br></div><div><br></div><br></font></span></div></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">-- Milo<br>===================================================<br>National Magnetic Resonance Facility at Madison<br>
An NIH-Supported Resource Center<br><br>W. Milo Westler, Ph.D.<br><br>NMRFAM Director<br>Senior Scientist<br> and<br>Adjunct Professor<br>Department of Biochemistry<br>University of Wisconsin-Madison<br>DeLuca Biochemistry Laboratories<br>
433 Babcock Drive<br>Rm B160D<br>Madison, WI USA 53706-1544<br>EMAIL: <a href="mailto:milo@nmrfam.wisc.edu" target="_blank">milo@nmrfam.wisc.edu</a><br>PHONE: (608)-263-9599<br>FAX: (608)-263-1722<br>======================================================================= ========</div>
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