[gmx-users] index file

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 12 01:37:00 CEST 2011

On 12/05/2011 8:23 AM, ahmet yıldırım wrote:
> Dear users,
> I have two ligands. I created a special index group that merges the 
> protein, LiGA and LİGB.
> I have the pr.mdp file as the following:
> ...
> energygrps      = Protein    LİGA_LİGB
> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
> ...
> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
> Fatal error:
> Group LİGA_LİGB not found in indexfile.
> I get the fatal error since I dont have a special index group that 
> merges LiGA and LİGB. should I create two different index file?

You need to give grompp an index file that defines all the groups you 
use. Yours didn't define LIGA_LIGB, so you need to do so, or to change 
your energygrps


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