[gmx-users] WARNING: negative index -1 in group System

[Christopher Rowan]

Hi,

Allow me to be the first to archive a message with "negative index".

I ask for an index file:
make_ndx_s -f ???.pdb -o ???.ndx
and specify:
a AG
to select all the silver atoms into a group.
The index file then clearly numbers and lists the atoms: all in [
system ], again all atom numbers in empty brackets [   ] and then my
silver atoms in the [ AG ] group.
I proceed to define a box:
editconf_s -f ???.pdb  -n ???.ndx -o ???.gro -bt cubic

The output gives:

...
Select a group for output:

WARNING: negative index -1 in group System


WARNING: negative index -1 in group System

Group     0 (      System) has    68 elements
Group     1 (          AG) has    13 elements
Select a group: 0
Selected 0: 'System'
Segmentation fault

Perplexing.

I found Travis Trudeau's message about having a zero index and tried
finding atom numbering:
grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx

But again got:

...
initialising group options...
processing index file...

WARNING: negative index -1 in group System


WARNING: negative index -1 in group System

Making dummy/rest group for T-Coupling containing 33 elements
...

So, if anyone could shed some light on how to overcome the negative
index hurdle it would be much appreciated,
Chris Rowan
University of Victoria