[gmx-users] best structure

[Pim Schravendijk]

Apparently, there is a program to do statistical analysis on the 
possibility of getting a cis or trans conformation for your peptide bond 
(I don't have any experience with it, though):

http://www.fmp-berlin.de/nmr/cops/

corresponding article:

http://www.bioinformatics.oupjournals.org/cgi/content/abstract/bti089v1

--
Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research
http://www.mpip-mainz.mpg.de/~schraven/

On Sat, 12 Feb 2005 gmx-users-request at gromacs.org wrote:
> From: UCT Staff Member - Jackson <Jackson at SCIENCE.uct.ac.za>
> Subject: Re: [gmx-users] best structure
> Date: Fri, 11 Feb 2005 08:31:26 +0200
> 
> To try and get arround this I did vacuum dynamics at 600K at which
> temperature I did get some cis/trans isomerization.  From this I ended
> up with 3 low energy conformers, (1) all trans,(2) one cis bond and (3)
> two cis bonds.
> 
> It is unlikely that in nature you would get any cis/trans isomerization
> but it is possible that during the synthesis a cis isomer is produced.
> 
> Can you make any suggestions?
> 
> Thanks
> Graham