[gmx-users] Fatal error:Chain identifier
Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 29 19:07:24 CET 2010
ahmet yıldırım wrote:
> 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.
>
That depends on whether you need this residue, hence all of my previous
questions. If there is some functional significance to this residue and you
need it for a simulation, then you'll either need to deal with the .rtp file,
which actually is not terribly difficult, it just involves a little bit of
reading and studying existing examples. Otherwise, if the molecule is
non-covalently bound to the protein, follow the tutorial I linked before, and
pay attention to the hint I gave you before about using PRODRG, which I will
reiterate more explicitly: the output topology from PRODRG will require manual
modification and validation.
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-Justin
> Thanks for your help
>
> 29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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> <mailto: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>>
> <mailto: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>>>
> <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
> <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 <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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