[gmx-users] Fatal error:Chain identifier

[Justin A. Lemkul]

ahmet yıldırım wrote:
> You said "You do not have to make changes in pdb file".

When did I say that?

> Then How will I create .rtp file.
> 

That depends entirely upon what that residue is.  Is it a constituent residue of 
the protein, such that its backbone is incorporated in the protein structure? 
Is it connected via a sidechain?  Or is it a ligand?  Any or all of the 
following might apply:

http://www.gromacs.org/Documentation/File_Formats/.rtp_File
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
http://www.gromacs.org/Documentation/File_Formats/specbond.dat
http://www.gromacs.org/Documentation/Tutorials#General (Drug-enzyme complex, 
although beware the use of PRODRG)

And, of course, the manual, which describes the contents of the .rtp file more 
thoroughly.

-Justin

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

-- 
========================================

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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