Dear Amber Developers,
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.
Do I have to do the free energy correction as suggested in the
Warren's paper? Please provide me some information regarding this
issue.
Thanks,
mani
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Received on Fri Jul 20 2012 - 14:30:17 PDT
