VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Mar 19 2006 - 14:51:49 CST

Hi Brian,
could you please send me the topology file and script you used to run
the psfgen standalone on this structure? I am able to reproduce this
error, so if you send me the rest of that data I should be able to fix it.
Many thanks,
Peter

Brian Bennion wrote:

>
> 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
> ************************************************