Hi,
Check out the method used in:
How to Obtain Statistically Converged MM/GBSA Results
SAMUEL GENHEDEN, ULF RYDE, J Comput Chem 2009
On 14 October 2010 10:59, Lars Skjærven <lars.skjarven.biomed.uib.no> wrote:
> Dear Amber users,
> I'm attempting to measure the binding free-energy of a protein-protein
> complex. Ligand binding to each of the two protein subunits are assumed to
> weaken the binding energy between them.
>
> Thus, I performed 6 MD simulations of the complex with the two ligands, and
> 6 MD simulations without the ligands. All simulations are 50 ns long.
> MMPBSA
> was then used on each of the simulations to measure the binding free energy
> in the two cases. 500 frames from each of the simulations were used in the
> MMPBSA calculation.
>
> I'm seeking some advice in how to interpret the results I get here. Also,
> does it make sense to include the ligand in the MMPBSA calculation.
>
> The MMPBSA "setup" and results are listed below. They show a small decrease
> in the binding energy upon ligand binding. However, the variation in each
> of
> the measurements seems to be quite large.
>
> Any help is greatly appreciated.
>
> Kind regards,
> Lars Skjaerven
>
> MMPBSA setup:
> =Case 1=
> "Complex": protA+ligand+protB+ligand
> "Ligand": protA+ligand
> "Receptor": protB+ligand
>
> =Case 2=
> "Complex": protA+protB
> "Ligand": protA
> "Receptor": protB
>
>
> The results of the calculations are as follows:
>
> =Case 1=
> 1. DELTA G binding = -67.2979 +/- 9.0536
> 0.4049
> 2. DELTA G binding = -70.5699 +/- 11.1792
> 0.4999
> 3. DELTA G binding = -74.2973 +/- 12.5725
> 0.5623
> 4. DELTA G binding = -67.2641 +/- 9.4797
> 0.4239
>
> =Case 2=
> 1. DELTA G binding = -79.1609 +/- 8.6845
> 0.3884
> 2. DELTA G binding = -81.9272 +/- 13.0194
> 0.5822
> 3. DELTA G binding = -101.2126 +/- 13.0454
> 0.5834
> 4. DELTA G binding = -73.0323 +/- 10.4127
> 0.4657
> 5. DELTA G binding = -84.3521 +/- 8.7197
> 0.3900
> 6. DELTA G binding = -68.2018 +/- 8.1628
> 0.3651
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Received on Thu Oct 14 2010 - 04:30:04 PDT
