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

[Carlos Navarro]

Hi Mark
Thanks for the reply.
I called make_ndx as following:
gmx make_ndx -f system.gro -n system.ndx -o system.ndx. I don’t know a
different way to call it.
What things/parameters can I obtain from a *tpr file that are more
difficult (or impossible) to obtain from a *gro file?
With respect to gmx select. I don’t have to much of experience working with
the tool. So I’ll take a look at the —help to see how the tool could help
me with my problem.
Thanks again,
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

On September 27, 2017 at 9:57:11 AM, Mark Abraham (mark.j.abraham at gmail.com)
wrote:

Hi,

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.

Mark

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

> 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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