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

[Christopher Rowan]

Sorry to post again,

But I meant to say that for atom indexing I looked using gmxdump:

gmxdump_s -s ???.tpr -f ???.pdb -nr

and found only indexing starting at zero; e.g

atom[0]={name="AG"}

Cheers,
Chris Rowan
University of Victoria





2009/6/23 Christopher Rowan <chriskrowan at gmail.com>:
> 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
>