[gmx-users] Fatal error:Chain identifier

[Justin A. Lemkul]

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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