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

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Mark Abraham ha scritto:
>>> 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?
> 
> make_ndx is the tool for generating such groups. If you read make_ndx -h
> you'll see it does indeed let you create groups based around chain IDs,
> but that'd (at least) require supplying it with a coordinate file that
> has chain IDs. You could do that, but doing the house-keeping to assign
> those IDs is tricky, and with PDB you're probably limited by 26 letters.
> make_ndx will also let you create a group according to a range of atomic
> numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to
> preserve/create chain IDs. Since you only need to create index groups
> once for a given coordinate file, that's not too onerous. If you will
> have lots of simulations with different numbers of such groups then you
> might write a script to automate that... see
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
> 

Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do
you mind if I later I try to update the "multiple chains" wiki page
based on your advices?

>>> 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 :)
> 
> Sure. Doing some "irrelevant" tutorial material can be useful
> introductions to the workflows. Regard;ess, the learning curve can be
> steep for all computational chemistry software. Unfortunately no
> beginner these days seems to want to come in and just do
> protein-in-water :-) That makes their life hard.

Yep, unfortunately that's kinda not simply "protein-in-water". I am
trying to understand all pieces I need very slowly, step-by-step. And I
guess you will hear my cries often in this ML :)

Thanks again,

m.