[gmx-users] Error when using AFM Pulling

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Feb 23 10:57:07 CET 2006


Hi

Is your com-group in the index-file?
Would be helpful to see:
pullout.ppa
pull.ppa
index.ndx
mdp-file

I think, after inspecting those, we can handle your problem

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Bob Johnson wrote:
> Hello everyone,
> I'm trying to use AFM pulling. I am entering the following command:
> 
> mdrun -s topol.tpr -o pull.trr -c pull.g96 -e pull.edr -g pull.log -pi pull.ppa
> -n index.ndx
> 
> The .ppa file looks like this:
> verbose = no
> runtype = afm
> group_1 = DA
> ;group_2 = nanotube
> reftype = com
> pulldim = N N Y
> afm_rate1 = 0.0005
> afm_k1 = 1000
> reference_group = nanotube
> 
> The index file looks like:
> 
> [ nanotube]
> atom numbers
> 
> 
> [ DA ]
> atom numbers
> 
> However, I get the following message:
> 
> Fatal error: No groups in indexfile
> 
> I don't understand this message because I have several groups defined in the
> index file. What is the problem?
> 
> Thanks,
> Bob Johnson
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