[Chimera-users] scan and minimization of dihedral angle

[Eric Pettersen]

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 at 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 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
>        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 at nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
> ======================================================================= ========
> <PE_scan.pl><pot_energy.pl>

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