[gmx-users] pdb2gmx problem

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 6 17:02:52 CEST 2009

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?


>                    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


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