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

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 14 14:11:48 CEST 2009

ms wrote:
> 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.
> Thanks!
>>> - 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?

They can, but you have to define them.  If there are multiple protein chains in 
the system, the Gromacs tools will define them as one group - 'Protein' - and 
not distinguish between them.  This is a rather easy problem to solve, though, 
without even using chain identifiers.  You can create index groups based on 
residue numbers to define each chain, then it doesn't matter what format the 
coordinate file is in.  For example, you can define groups like:

r 1-37
r 38-299



>> 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 :)
> m.
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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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