[gmx-users] Fatal error:Chain identifier

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. Where is the error?

Pdb file:

ATOM      1  N   ALA A   4
ATOM      2  CA  ALA A   4
....
ATOM   2688  N   ALA B   4
ATOM   2689  CA  ALA B   4
....
ATOM   5449  OXT GLN B 361
TER    5450      GLN B 361
HETATM 5451  OAAABSG A   1
HETATM 5452  OABABSG A   1
....
HETATM 5474  OAAABSG B   2
HETATM 5475  OABABSG B   2
....
HETATM 5492  O   HOH A   2
HETATM 5493  O   HOH A 362
HETATM 5494  O   HOH A 363
....
HETATM 5744  O   HOH B 362
HETATM 5745  O   HOH B 363

29 Aralık 2010 19:12 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Mark,
>>
>> The chain identifier have continuous. In sequence does not show any
>> problem.
>>
>>
>>
> Then you're not looking at the right contents; pdb2gmx wouldn't complain
> otherwise.  Usually HETATM entries like HOH (water) are after all protein
> chains, so you might have chains A, B, C, etc for protein followed by A, B,
> C, etc for water.  Have a more thorough look through the .pdb file.
>
> -Justin
>
>
>> 29 Aralık 2010 15:10 tarihinde Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> yazdı:
>>
>>
>>    On 29/12/2010 10:12 PM, ahmet yıldırım wrote:
>>
>>        Dear users,
>>
>>        ab at ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p
>>
>>        Select the Force Field:
>>        5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>
>>        Fatal error:
>>        Chain identifier 'A' was used in two non-sequential blocks
>>        (residue 710, atom 54 49)
>>
>>        What should I do to correct this error?
>>
>>
>>    Look at the entries whose chain identifier is A, and see why they
>>    are non-sequential, and take suitable action to remedy. You may need
>>    to Google for the PDB file format if you don't already understand it.
>>
>>    Mark
>>
>>
>>
>>        Thanks in advance
>>
>>        --         Ahmet YILDIRIM
>>
>>
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>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Ahmet YILDIRIM
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