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 <[email protected]> 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: [email protected] or [email protected] > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
