[gmx-users] interaction energy

pratibha kapoorpratibha7 at gmail.com
Sun Mar 30 16:56:40 CEST 2014

Hi all,
I would like to calculate LJ and coulombic interaction energy between
protein backbone and ligand And also between protein sidechain and ligand. I
am able to calculate interaction energy between protein and ligand by
specifying these groups in *.mdp file, creating tpr, using mdrun -rerun
option and finally using g_energy. But I am unable to understand how to
dissect this contribution into protein backbone and sidechain?
If I specify energygrps as Backbone LIG,
then I am getting following error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in
different energy groups
which I understand (from previous posts) comes when we remove any group
necessary for other functions (although we dont need these in our energy
So, then I have specified following energy groups in my *.mdp file:
Protein Backbone LIG
But now I am getting following error:
Atom 1 in multiple Energy Mon. groups (1 and 2)

My question is how can I calculate protein's backbone and sidechain
interaction energies with the ligand separately?

Thanks in advance.

View this message in context: http://gromacs.5086.x6.nabble.com/interaction-energy-tp5015478.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list