[gmx-users] merge two PDBs

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 30 15:25:11 CEST 2009

Peyman Yamin wrote:
> Hi everyone,
> can one still search the mailing list entries? I can't find it in the new
> site!

I've posted this several times in the last few days:


> A question: what would one want to do if he had a PDB file of a dimer and
> pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried
> to separate two mers and then pdb2gmx'ed them getting nice topologies of each.
> But how can I merge them together again? the numbering will be messy. There
> should be some more human way for that :-) Editconf does not take two files
> and I don't want to put the other one at a random position since it needs to
> be just beside the other mer! What should one do at all, if one gets a NMR-
> based PDB which has the structure of more than one chemically equal species
> and wants to work with it?

Concatenate the files using standard *nix utilities like cat, remove any 
repeated/unnecessary box information or REMARK lines, and use genconf to renumber.


> With Herzian thanks...
> Cheers,
> Peyman
> --
> Peyman Yamin
> Institut fuer Strukturbiologie und Biophysik (ISB)
> ISB-3: Strukturbiochemie
> Forschungszentrum Juelich
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> mailto: p.yamin[at]fz-juelich.de
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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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