OXT in pdb file

From: nisha_at_ncbs.res.in
Date: Tue Jul 04 2006 - 05:09:51 CDT

Hi Namd Users

I am unsure as to what to do with regard to the OXT atom and TER patch at
the end of a protein chain in the PDB file. I get the following warning
for the segment because no such OXT atom exists in the topology file I am
Warning: failed to set coordinate for atom O LYS:122 PRO0
Warning: failed to set coordinate for atom OXT LYS:128 PRO1

So I tried to use the LINK patch to link segments, however I get errors
such as below:
applying patch LINK to 1 residues
Warning: add bond failed in patch LINK
Warning: add angle failed in patch LINK
as well as many more warnings.

Kindly let me know where I am going wrong.

With thanks and regards

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