From: nisha_at_ncbs.res.in
Date: Fri Jul 07 2006 - 22:48:42 CDT
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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