VMD-L Mailing List

From: David E. Heppner (heppner_at_alumni.stanford.edu)
Date: Tue May 03 2016 - 15:29:22 CDT

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

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David E. Heppner
david.heppner_at_med.uvm.edu
heppner_at_alumni.stanford.edu
Department of Pathology and Laboratory Medicine
Department of Chemistry
University of Vermont