[gmx-users] how to include multiple energy groups for interaction energy calculation?

[sunyeping]

Dear all,

I am doing MD simulations on a protein-ligand complex. This complex has 4  protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to calculate the interaction energy between each ligand and their binding protein subunit, respectively. I include the  "energygrps" parameter in the mdp file for generating a tpr file for rerun the trajectory as following:
    energygrps      =  Protein LIG1

This seems to work fine. However, could it be possible to include all four ligands in the "energygrps" parameter and rerun the trajectory once to get the interaction energy between all the four ligands and their respective binding protein subunit? I tried to write the "energygrps" parameter as following:
  energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein LIG4
and run the "grompp" command:
     gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
I received the following error:
    Fatal error:
Group LIG1, referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

I am sure that LIG1 is included in the index file. This error is most probably caused by the incorrect input of the "energygrps" parameter in the mdp file. 

So I wonder whether it is possible to include multiple energy groups in the mdp file or I have to rerun the trajectory four times to get the interaction energy for the four ligands?

Thank you in advance.

Yeping Sun