20 Mar
2005
20 Mar
'05
6:11 a.m.
Hi, 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, Himanshu Grover