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|Energy terms in "epdb" output
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|Author:||gmst87324 [ Fri Oct 21, 2016 4:19 pm ]|
|Post subject:||Energy terms in "epdb" output|
I used epdb to calculate single-point energy of a complex. The result is as below, followed by a few questions:
epdb: USER Estimated Free Energy of Binding = -2.24 kcal/mol [=(1)+(2)+(3)-(4)]
epdb: USER (1) Final Intermolecular Energy = -2.70 kcal/mol
epdb: USER (2) Final Total Internal Energy = +0.16 kcal/mol
epdb: USER (3) Torsional Free Energy = +0.30 kcal/mol
epdb: USER (4) Unbound System's Energy = +0.00 kcal/mol
- The term (2) is the total energy from "Ligand Intramolecular Energy Analysis" table. In AutoDock 4.2, we have (V_bound_LL - V_unbound_LL) = 0 ; so why should term (2) contribute to the estimated free energy of binding if the two V_LL terms will cancel out each other?
- I suppose term (1) is "V_bound_PL", and term (4) is "V_unbound_PL". Is it right?
- If I was right in the second question, then where is the contribution of the two terms "V_bound_PP" and "V_unbound_PP" to the deltaG?
Thanks in advance for helpful comments!
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