[gmx-users] Swiss pdb viewer

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 22 23:02:06 CET 2011

ahmet yıldırım wrote:
> Dear Justin,
> Fatal Error:
> Chain identifier 'A' was used in two non-sequential blocks (residue 710, 
> atom 5449)
> I have sometimes this error for some pdb files.
> 1. Missing atom and residues entries, that GROMACS is unable to reconstruct.
> 2. HETATM entries which can not be processed using pdb2gmx.
> Solution:
> After I am reconstructing the pdb file using Swiss pdb viewer program 
> (that is, the program is doing fixes) , I am deleting the HETATM 
> entries, I can process it using pdb2gmx.
> Is this solution the right ? Are there disadvantages?

Modeling in missing atoms and residues is certainly necessary.

Removing HETATM entries depends entirely upon what those molecules are.  pdb2gmx 
can process HETATM or ATOM entries, so I suspect that the content of those 
HETATM entries is what is causing a problem.  If these problematic residues are 
artifactual crystallization solvents, ions, etc, then probably you can delete 
them.  If they serve some functional role (e.g., drug molecule, cofactor, etc), 
then you can remove them for the purpose of running pdb2gmx, but you'll 
eventually have to deal with them somehow.


> -- 


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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