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