RE: OXT in pdb file

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Jul 08 2006 - 01:32:31 CDT

Since it's only the last two atoms of your protein, you could get away with
letting psfgen guess their coordinates. Alternatively, you could manually
edit your pdb file to change the names of just those two atoms (from O to
OT1 and OXT to OT2) and then run psfgen.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of nisha_at_ncbs.res.in
Sent: Friday, July 07, 2006 10:49 PM
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: OXT in pdb file

Hi

Thanks for your help. However, am still unable to get it right.

1. Without aliasing the OXT i get the following warning:
Warning: failed to set coordinate for atom O LYS:122 PRO0
Warning: failed to set coordinate for atom OXT LYS:122 PRO0

2. And, when I alias only OXT to OT2 (eg. pdbalias atom LYS OXT OT2), i
get the following warning:
Warning: failed to set coordinate for atom O LYS:122 PRO0

3. However, I do not know how to alias the first O to OT1, and the OXT by
OXT2 (I tried for eg. pdbalias atom LYS O OT1 and pdbalias atom LYS OXT
OT2) only for the selected residue; It works for the residue containing
the OXT atom, however for all other residues containing O atoms, I now get
the following warnings:
Warning: failed to set coordinate for atom O ALA:1 PRO0
Warning: failed to set coordinate for atom O LYS:2 PRO0

Kindly let me know where I am going wrong.

With thanks and regards
Nisha

> 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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