[gmx-users] genbox

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 20 13:10:59 CEST 2010

fahimeh bafti wrote:
> Hello,
> I want to use a file.pdb which has 8 chain of polypeptide, each chain 
> contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I 
> need to add 4 chains or in the other word 24 residues. I think I have to 
> use genbox, so I make another copy of  file.pdb and rename it to 
> insert.pdb and i used this command, but it doesn't work.
>  genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro
> can anybody help me?

The implication with genbox -ci -nmol is that the coordinate file passed to -ci 
contains one molecule, and an additional -nmol molecules are inserted.  So if 
you already have 8, you need a coordinate file with one polypeptide and then:

genbox -ci insert.pdb -nmol 4

Note in the documentation that -nmol refers to the number of molecules, not a 
number of residues, which I think is the root of your problem.


> Fahimeh
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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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