[gmx-users] question about make_ndx

Ullmann, Thomas thomas.ullmann at mpibpc.mpg.de
Thu Apr 4 18:51:06 CEST 2019


Under Unix/Linux you can use

gmx make_ndx -f struc.gro -o test.ndx << _EOR_
r 1


R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullmann at mpibpc.mpg.de

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Carlos Navarro <carlos.navarro87 at gmail.com>
Sent: Thursday, April 4, 2019 5:55:26 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] question about make_ndx

Dear gmx users,
I’m trying to feed make_ndx though echo, but I’m having some issues.
When I use echo  "r 1"  | gmx make_ndx -f struc.gro -o test.ndx I got the
following error message:

Fatal error:
Error reading user input

So apparently I have to include also the q argument to close properly
make_ndx, but I don’t know how to do this.
I have tried with echo  "r 1 q"  | gmx make_ndx, echo  "r 1” “q"  | gmx
make_ndx, and other combinations, but non of them worked.
Any ideas?
Best regards,

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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