VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Mar 17 2006 - 16:39:15 CST

Hello,

I have been testing the new features in 1.8.4b11 (sorry I know I am one
behind) for windows and noticed that placement of hydrogens on the
branching Carbon of Leucine sidechains is placed parallel to the axis of
the Cbeta-Cgamma carbon bond.
ie
         CH3
        /
Ca-Cb-HCg
        \
         CH3

instead of something more reasonable like...

         CH3
        /
Ca-Cb-Cg-H
        \
         CH3

Attached are the before and after pdb files. If these hydrogen placements
are left in the current position the miniziation will fix them but often
requires MAJOR side motions...

I haven't seen this behavior in older standalone psfgen use.

Brian

************************************************
   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-448 bennion1_at_llnl.gov
   7000 East Avenue phone: (925) 422-5722
   Livermore, CA 94550 fax: (925) 424-6605
************************************************