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PostPosted: Fri Oct 21, 2016 4:19 pm 
Millimolar User
Millimolar User
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Joined: Tue Oct 18, 2016 6:40 pm
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Hi all,

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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