[AMBER] MMPBSA Calculation

From: Preeti Pandey <preetipandey2806.gmail.com>
Date: Mon, 21 Nov 2016 22:19:43 +0530

Hello Amber Users,
I have simulated a dimeric protein complex containing two ligands (both the
ligands are same). Now I would like to calculate binding energies (MMPBSA
So, in this case, binding energy can be calculated as:

                                                                   ΔG = ΔG
complex - ΔGreceptor - (ΔGL1 + ΔGL2)

I am confused with how to carry out the above calculation. Can I take into
account both the ligands at the same time? Is it the correct way?

I have gone through earlier mails where it was suggested to define either
one of the ligands with the complex and calculate for the second one or
take into account one of the ligands with the receptor i.e.

First Way:
    ΔG = ΔGrecepor +L1 - ΔGreceptor - ΔGL2
    ΔG = ΔGrecepor +L2 - ΔGreceptor - ΔGL1

Second Way:
  ΔG = ΔGrecepor +L1+L2 - ΔGreceptor+L2 - ΔGL1
  ΔG = ΔGrecepor +L1+L2 - ΔGreceptor+L1 - ΔGL2


*Regards *
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Received on Mon Nov 21 2016 - 09:00:03 PST
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