[gmx-users] monitoring trans-cis transition of proline residue

[Shang-Te Danny Hsu]

Hi GMX users,

I am trying to monitor spontaneous tran-cis transition of a proline 
residue with a peptide starting from an extended conformation with the 
proline residue bearing either trans or cis configuration. Using default 
pdb2gmx I got the same topology files for both (trans and cis) peptides 
and the cis form quickly switched to a trans form after a short md 
equilibration. It is presumably due to the definition of a trans 
configuration of proline within the topology file.

Has anyone done such simulation to derive the ratio of between trans and 
cis forms of a proline residue? Although someone has reported appearance 
of an undesired cis form at high temperature (1000K), I would like to 
simulation the system at low temperature (ca 280K) and the energy 
barrier is unlikely to be overcome with the default setting.

Cheers,
-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl