Christopher Rowan wrote:
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.
First, it would be helpful to know which version of Gromacs you're using,
especially if this is a bug in an older version. If it is the most current
version (4.0.5), it is of much greater interest :)
What I don't understand is why you have a group with no name; that shouldn't be.
If you're defining AG atoms, then you should have [ System ] and [ AG ].
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
I'm assuming you've check the entire [ System ] directive to ensure that all
indices are positive? With the generation of a "no-name" group, it is possible
that something funky is going on.
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
Does the command work without the index file? If you're specifying a box to
contain the entire system, then you shouldn't need the index file.
-Justin
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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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