[gmx-users] best structure

Pim Schravendijk schraven at mpip-mainz.mpg.de
Sat Feb 12 12:46:25 CET 2005

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):


corresponding article:


Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

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

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