cis proline

Xin Jia xjia at LJCRF.EDU
Wed Nov 20 18:51:40 EST 1996



Dear xplor users:

I have a question about cis- proline conformation in the structure
calculations.  I found if a proline residue is a trans- conformation, 
the calculation is fine. But if it is the cis-, after refinement, 
it turn to be a distorted trans- with some typical distance violations.
The topology files I have used were either topallhdg.pro from the
standard xplor library or the one modified by Dr. Michael Nilges
for improving prolines. These topallhdg.pro files include patches
which allow the convertion from trans- to cis- peptide bond.
As a control, I have also used the program "Discover" (Biosym) to
refine the structure. I got almost perfect cis- conformation from
the same starting structure and experimental constraints.
I wonder why? Any comment and suggestion will be very helpful.
Thanks in advance.

Xin Jia
La Jolla Cancer Research Center
The Burhman Institute






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