On Tue, Apr 21, 2015 at 9:58 PM, windy <chxp_moon.163.com> wrote:
> Hi, Jason:
>
> Thanks for you reply . I finaly using the same frames to calculate
> the free energy.
>
> What you reply that we are using MMPBSA.py to compute a binding free
> energy for a noncovalent protein-ligand complex, and that you only care
> about that binding free energy.
>
> But my system is a convalent protein-ligand complex, may I use the
> MMPBSA.py to calculate the free energy ?
No.
> Is the result reasonable enough to make others trust on?
>
> What I need to be care when using MMPBSA.py to calculate a convalent
> protein-ligand complex ?
>
>
MM/PBSA does not apply to covalent complexes. If you look at the
thermodynamic cycle that MM/PBSA is based on, you can see that it does not
account for any broken or formed bond(s).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 22 2015 - 04:30:02 PDT
