[gmx-users] Membrane protein tutorial

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 9 06:44:43 CEST 2009

Pawan Kumar wrote:
> Hello sir,
> Thanks for such a explanatory tutorial.
> I am stuck with one error now.
> I have protein, popc, sol and cl- in my system.
> I have merged the sol and cl- using make_ndx.
> But when I run grompp I get the error like this "popc not defined in the 
> index file".
> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o 
> box_pr.tpr

As I said last time, you'll need to give grompp the index file so that 
it can make sense of your use of the new group(s) name(s).


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