First, since your set ups of your MD simulations are different, it's not
suprising to see some difference of binding energy. If you include
entropy, that discrenpacy may be reduced.
Second, MM/PBSA is good for calculating relative binding free
energies. I'm not so sure about values of absolute binding free energies
obtained from MM/PBSA.
Third, the total MM energy can be very different if your systems in the MD
simulation are quite different (box vs. cap).
hope this helps,
Wei Wang
> Dear amber users,
>
> I am running mm_pbsa calculation for two MD simulation results for the same
> system to obtain binding energy information between ligand and protein. One
> MD simulation consider all system (protein+ligand+water box) and another
> simulation only consider active site proteins and the atoms within 20 A of the
> active site proteins (with the other atoms fixed during the MD simulation).
>
> The mm_pbsa calculated binding energy for the full sys is -161 +/- 14 kcal/mol
> and the binding energy for the other system is -168 +/- 14 kcal/mol. Are
> these values reasonable good for two same system with different MD treatment?
>
> Another question, the calculated absolute energy for these two system is total
> different. In full system, the average calculation energy for protein, ligand
> and complex (protein+ligand) are -7456, -120 and -7745, respectively.
> In another system, the average calculation energy for protein, ligand and
> complex (protein+ligand) are 174491, -15, 174309, respectively. I am not
> quite sure what cause the absolute energy so different. Is there any
> suggestion? Thanks in advance.
>
> Wentao Fu
> Ctr. Pharm. Biotech.
> University of Illinois at Chicago
>
Received on Mon Nov 19 2001 - 17:27:10 PST
