From: surendra negi (negi009_at_yahoo.com)
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.
sn
--- nisha_at_ncbs.res.in 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
>
>
>
>
>
>
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