[gmx-users] pdb2gmx problem

[Tsjerk Wassenaar]

Hi Abhijit,

I think the Zinc ion goes with chain B and uses the same identifier.
Given the fact that you didn't quite understand the error, and found
it necessary to post a question, this raises another question: should
you be wanting to simulate a protein with a zinc ion?
(http://www.gromacs.org/WIKI-import/Exotic_Species).

Cheers,

Tsjerk


On Tue, Oct 6, 2009 at 5:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> abhijit kayal wrote:
>>
>> Hello everyone
>> I am going to analysis the PDB file  3GJN.pdb.After giving the pdb2gmx it
>> shows the fatal error
>>
>> "chain identifier 'B' was used in two non-sequential blocks (residue 404,
>> atom 3227)".So what is the solution for this.
>>
>
> The error message is quite clear, even telling you where the problem is!
>
> Make sure chain identifiers are continuous.  Have you inserted or deleted
> anything?  Dealing with ligands or co-solvents that might be arranged oddly?
>
> -Justin
>
>>                   Thank you
>>
>>                 Abhijit
>>
>>
>> ------------------------------------------------------------------------
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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