[gmx-users] index groups

[Moeed]

*I read thorough the manual on index groups and creating index file. This is
the command I tried:

make_ndx -f index.gro -o index.ndx
*
with index.gro you proposed:

[ special ]
  1  3
[ all ]
  1  2  3  4

error I get:

Reading structure file

-------------------------------------------------------
Program make_ndx, VERSION 4.0.7
Source code file: confio.c, line: 728

Fatal error:
Invalid line in index.gro for atom 1:
[ all ]
-------------------------------------------------------

I thought maybe the group name should be changed... but it is complaining of
sth I cant figure out.

Also I am asking the following Q just for the sake of learning. I dont want
to do something blindly :)
- can you please let me know what is the justification behind using 1 3 in
first group.  *
*- I read about default groups. like "system" where all atoms are defined.
So why do we need to define "all" group again? *

Thanks,
*
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