[gmx-users] Membrane protein tutorial

[Mark Abraham]

Pawan Kumar wrote:
> Hello Mark Sir,
> 
> I have tried that way also.
> The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p 
> topol.top -o box_pr.tpr
> But this time i get an error like this "Atom 1 defined in multiple 
> groups (1 & 3). "
> How to overcome this error ?

You can't have the same atom in multiple groups used for the same 
purpose within mdrun (e.g. T-coupling or energy). I guess you've 
constructed your index file in a manner that is inconsistent with your 
use of it.

Mark