[gmx-users] What is best way to get multiple chains?

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 13 23:18:23 CEST 2009

ms wrote:
> Hi,
> I am a gmx newbie, so please don't bite too much! :)
> Learning gmx, I am experimenting with simulations with multiple
> identical small chains. What I did was:
> - I generated the peptides with pymol
> - Generated a .gro with pdb2gmx
> - Used editconf to create translated copies
> - Stitching them together and creating the complete file, adjusting
> numbers etc. manually
> It worked well, but the chains are not recognized as *different* chains
> -which could be useful. Documentation says I should use another format
> like the pdb, but it is a bit sparse on the subject. I think I can use
> pdb instead of gro if needed, but does this also work when creating
> boxes etc.? Isn't there a way to get chain identifiers in a gro file?
> What is best practice?

You can use .pdb format just fine.  There is no requirement that you use .gro, 
and in fact the format specification of .gro does not include a field for chain 
identifier, so no, there is no way to include chain identifiers in a .gro file.


> Thanks a lot,
> Massimo
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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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