[gmx-users] make_ndx not working

[Camilo Calderon]

Hello all,

I am trying to generate an index file for a box of solvent, and I must be
missing a key detail somewhere...
The following is the command that I am using:

make_ndx -f conf.gro -o index.ndx

The conf.gro that I am using is the same as one of those provided in the
'top' folder, which is included in the GROMACS distribution.  The program
starts, but fails to see the individual atoms that are in each residue.  In
other words, the index.ndx that is produced is a trivial one - all it
produces is a list with every single atom number in the configuration file.
What is missing here?  Why does make_ndx not see the individual atoms in the
configuration file?

Thanks to all for any responses!

Camilo
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