OXT in pdb file

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Sep 25 2008 - 13:38:06 CDT

I have a question regarding the message in the archives (Attached below):
Do we ened to alias the OXT in the pdb file? The NAMD tutorial didn't and runing it the way it is in the tutorial, NAMD seems to automatically change it from OXT to OT

Thanks
Rabab

Re: OXT in pdb file

From: surendra negi (negi009_at_yahoo.com)

Date: Wed Jul 05 2006 - 15:16:12 CDT

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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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