[gmx-users] Fatal error:Chain identifier

[ahmet yıldırım]

You said "You do not have to make changes in pdb file".
Then How will I create .rtp file.

29 Aralık 2010 19:32 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> 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
>>
>
> Right here.  You're going from the end of chain B to the beginning of chain
> A, then back to B later on.  Also realize that whatever "ABSG" or "BSG" is,
> it won't be recognized by pdb2gmx unless you've built a proper .rtp entry
> for it.
>
> -Justin
>
>  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 <mailto:
>> 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>
>>        <mailto: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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>
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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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