I am trying to model a protein complex, with 2 chains. I wish to know
the interaction energy between the two chains at the end of
model-generation. Is it possible to do this, taking into account both,
van-der-waal's interactions as well as coulombic? Is the energy value,
that appears at the top of each generated model pdb file, indicative
of the same (While optimizing the structure, I have Dynamic Lennard
and Dynamic Coulomb switches on, and others off.)
I am not looking for the internal energy of the whole protein complex, but
just the interaction energy of the 2 comprising chains.
Any help would be appreciated.
Thanks and regards,