Hi All,
I found this problem (the total energy from adding up the per-residue
decomposed energies deviate far from that in a normal non-decomposed PB
calculation) *happens only when I include explicit water molecules in the
decomposed PB caculations*. And the reason for the problematic PB total
energy from adding up the per-residue decomposed energies is that *all the
decomposed vdw and electrostatic energies for the included water molecules
are all ZERO!* But the sum of the decomposed polar solvation energies and
MM energies are very close to the non-decomposed ones.
I tried it on different systems. And it only happens when there are
explicit water molecules in the decomposed PB calculation. For decomposed
GB calculations, it works fine.
Could anyone shed some light on this issue please?
Great thanks!
Qiong
On Thu, May 10, 2012 at 4:17 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Hi All,
>
> I tried to calculate the binding free energy between molecule A and
> molecule B with both MMPBSA and MMGBSA methods. Also I did per-residue
> decomposition with both MMPBSA and MMGBSA, and then tried to calculate the
> binding free energy from per-residue decomposed energies. The following are
> the results.
>
>
>
>
> PBSA
>
> PBSA-decomp
>
> GBSA
>
> GBSA-decomp
>
> Complex
>
> -358.5
>
> -183.2
>
> -400.3
>
> -403.5
>
> A
>
> -305.6
>
> -215.7
>
> -357.0
>
> -361.8
>
> B
>
> -17.9
>
> -20.0
>
> -13.5
>
> -12.9
>
> Binding
>
> -35.0
>
> 52.5
>
> -29.8
>
> -28.7
>
> For MMGBSA, the binding free energy from these two approaches is quite
> close (-29.8 vs -28.7 kcal/mol).
>
> However, for MMPBSA, the binding free energy calculated from the
> per-residue decomposed energies is problematic (positive 52.5 kcal/mol). I
> understood that the non-polar solvation free energy cannot be decomposed in
> PBSA. But that energy also only makes a minor contribution to the total
> energy and binding. And the total energy from adding the per-residue
> contribution is far less than the non-decomposed one (take A for example
> -215.7 vs. -305.6 kcal/mol). Then what is the main reason leading to this
> problem of MMPBSA please?
>
> Could anybody shed some light on this issue please? Any suggestions will
> be greatly appreciated.
>
> Regards,
>
> Qiong
>
>
>
>
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Received on Fri May 11 2012 - 08:00:03 PDT
