make_ndx does not work
Using either of the 'a' or 'r' or 't' options do not work anymore in the master version of make_ndx.
This could be related to a patch removing the NOTSET construct from legacyheaders/types.
gmx make_ndx -f conf.pdb << EOF
reproduces the problem.
Fixes newly introduced bug in make_ndx.
After cleanup removing "NOTSET" from general include files a bug
was introduced in make_ndx not being able to generate groups
based on atom name, residue name or atom type.