On Sat, Jul 21, 2012, manikanthan bhavaraju wrote:
>
> I have performed TI calculations (explicit solvent) for the
> protein-ligand system using amber8 and the ff99 force field under
> periodic boundary conditions and NVT conditions. The ligand has +2
> charge, the ligand and its image in the next box might repel each
> other during the simulation. Since sander uses PME to handle
> electrostatic interactions. The charge on the ligand can the effect
> the final deltaA value. How is this handled in amber? I came across
> two articles regarding the infinite size corrections for PME during
> free energy calculations.
>
> 1. Warren and Patel, J.Chem.Phys. 127, 064509, 2007 refer to eq. 6 in page 6
> This paper recommends the free energy correction
>
> 2. Darden etal. J.Chem.Phys. 109, 24, 1998. refer eq. 2.24
>
> This paper recommends taking different boxes size, which I think
> "amber " implements.
This has been discussed before:
http://archive.ambermd.org/201112/0167.html
Note that the size of the corrections/extrapolations are very small for
+1 ions, and still should be small for +2 ions, assuming your box size is
not too small (which it won't be for a protein-ligand system.) Generally,
very precise TI calculations are required to see this behavior.
....dac
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Received on Sat Jul 21 2012 - 06:30:03 PDT
