Re: OXT in pdb file

From: surendra negi (
Date: Wed Jul 05 2006 - 15:16:12 CDT

Replace OXT by OT1. If you have already one Oxygen,
then replace first oxygen by OT1 and then OXT by OT2.
Hope this will rock.

--- wrote:

> 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
> using:
> 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
> Nisha

Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:48 CST