[gmx-users] Fatal error:Chain identifier

[Justin A. Lemkul]

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

========================================