VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue May 03 2016 - 16:29:00 CDT

Hi Dave,

Did you guess coordinates? If psfgen doesn't know where the atom is, and
you don't let it guess after regenerating angles and dihedrals, it will
place everything at the origin.

-Josh

On 05/03/2016 03:29 PM, David E. Heppner wrote:
> Dear All,
>
> I’m encountering a problem when trying to patch a phosphotyrosine
> residue with VMD. It seems to be a common problem, as seen in other
> posts, where the structure that is generated in NAMD has all three
> terminal oxygen of the phosphate at the same x,y,z coordinates.
> However, I cannot seem to correct this problem.
>
> The solution to this, as recommended, is to include “autogenerate
> angles dihedrals” or “regenerate angles dihedrals” after the patch
> command. For example,
>
> patch TP2 PROA:180
> regenerate angles dihedrals
>
> Even if this is included, NAMD gives a structure where the oxygen
> atoms are at the same x,y,z, coordinates. Please let me know if you
> have any suggestions of how to properly deal with this issue.
>
> Best,
> Dave Heppner
>
> ----------------------------------------------
> David E. Heppner
> david.heppner_at_med.uvm.edu <mailto:david.heppner_at_med.uvm.edu>
> heppner_at_alumni.stanford.edu
> Department of Pathology and Laboratory Medicine
> Department of Chemistry
> University of Vermont