Dear Amber Users,
I have calculated MM/GBSA interaction energy between two proteins and I
want to translate it into forces or attraction/repulsion and probably a
generation of torque. I was wondering about a couple of things:
1) Which terms in the MM/GBSA equation are force generating? My intuition
says SA term is not and should be excluded. Am I right?
2) If I have a potential energy of interaction of say -30 kcal/mol, how
much force will be generated between the two proteins?
3) If around the center of mass of the "ligand"-receptor ensemble, the
interaction energy is unevenly distributed, say 5 kcal/mol on one side and
25 kcal/mol on the other side, would that generate any torque? What
functional form can I use to calculate that torque? Is it the regular
torque or there is something I'm missing?
Any help will be appreciated.
Ahmed Ayoub
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Received on Wed Feb 18 2015 - 09:00:02 PST
