RE: OXT in pdb file

From: surendra negi (negi009_at_yahoo.com)
Date: Sun Jul 09 2006 - 11:09:38 CDT

Agree. Try to change it manually. Normally it is the
last residue.

--- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> 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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>
>
>
>
>
>
>

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