[gmx-users] Fatal error:Chain identifier
ahmet yıldırım
ahmedo047 at gmail.com
Thu Dec 30 13:37:21 CET 2010
Dear Justin,
Firstly, Thanks for your help. You said "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." How do you understand it? Where can I find
such an important theoretical information?
Thanks in advance
29 Aralık 2010 20:07 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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>>
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
--
Ahmet YILDIRIM
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