[gmx-users] Fatal error:Chain identifier

[ahmet yıldırım]

OK. if I do what sort change in pdb file, there is no need to create .rtp
file. It seems difficult to create the .rtp file.

Thanks for your help

29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> 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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-- 
Ahmet YILDIRIM
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