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

Carlos Navarro carlos.navarro87 at gmail.com
Wed Sep 27 14:43:30 CEST 2017

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 Navarro Retamal
Bioinformatic Engineering. PhD.
Postdoctoral Researcher in Center of Bioinformatics and Molecular
Universidad de Talca
Av. Lircay S/N, Talca, Chile
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

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