On Mon, Oct 19, 2015 at 5:22 PM, Renato Freitas <renatoffs.gmail.com> wrote:
> Hi all,
>
> I ran a 10ns MD simulation (all the topology files were made using the same
> procedures and the same force field) for a protein-ligand complex, and I
> used the MMPBSA.py script to calculate the binding energy. I noted that the
> 1-4 nonbonded interactions do not completely cancel out in the total
> binding free energy, resulting in a large positive value for deltaG.
>
> Can anyone tell me what could be the cause of this error?
>
Is your complex a covalent complex? MM/PBSA only works for noncovalent
binding events.
If not, visualize your receptor and ligand trajectories (generated by
MMPBSA.py -- _MMPBSA_receptor.mdcrd.0, ...) with the corresponding topology
files. I suspect you will find them incompatible with each other.
There are lots of ways to mess up MM/PBSA calculations, so it's hard to
guess which one happened here :).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 20 2015 - 07:00:05 PDT
