[gmx-users] Problems with make_ndx dealing with big systems

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 27 14:56:54 CEST 2017


I don't know the answer to your question as posed, because it looks like
you are confounded by limitations of the fixed-width .gro format, but you
didn't make clear how you were calling make_ndx. I would explore using more
useful file formats for such input, e.g. .tpr, and more powerful selection
tools, like gmx select.


On Wed, Sep 27, 2017 at 2:43 PM Carlos Navarro <carlos.navarro87 at gmail.com>

> Dear all,
> I have a system consisting of 361876 particles which correspond to double
> bilayer systems with a protein channel embedded in each one of them. Each
> protein channel is formed by two chains (A and B), and I want to make some
> analysis between both of the chains in each protein. I didn’t have problem
> to select specifically the atoms of chains A-B of protein ‘1’ and chain A
> of protein ‘2', unfortunately  since chain B of protein ‘2’ starts at atom
> 91740 and ends at atom 2540 I can’t select it in the same way I did with
> the other chains (in make_ndx: a ‘begging’-‘end’).
> Is there a way to select specifically only the atoms that form chain B in
> protein ‘2’ with make_ndx?
> Thanks in advance,
> Carlos
> ——————
> Carlos Navarro Retamal
> Bioinformatic Engineering. PhD.
> Postdoctoral Researcher in Center of Bioinformatics and Molecular
> Simulations
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
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