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

ms devicerandom at gmail.com
Wed Oct 14 14:10:12 CEST 2009

Mark Abraham ha scritto:
> 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.

Very much right. Thanks.

>> - 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.

This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?

> 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.

Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)


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