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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 14 01:27:12 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

This step is "generating a molecular topology". You don't need a .gro - 
it's just a regularized coordinate file produced as a side-effect.

> - Used editconf to create translated copies

Try genconf to do the replication. That should remove much of the manual 
labour. You would still probably need to edit in the chain IDs yourself, 
but that's easy work with a script or good editor.

> - 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?

What do you want the chain identifiers for? I'm not aware of a 
post-pdb2gmx purpose that they might serve.

If your system is N identical peptides in a solvent, then best practice 
for generating a complete .top is to generate one for a single peptide 
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a 
coordinate file which contains the N peptides' coordinates followed by 
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] 
section of the original .top to match. Other solutions are possible, but 
require more involved use of pdb2gmx, and might indeed want chain IDs.


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