Hi List,
I was reading a paper on Poisson-Boltzmann Solvents in Molecular Dynamics
Simulations by Jun Wang et al (2008). The paper talks about use of PB/GB
solvents with polarisation force fields is still in its infancy except few
examples with AMOEBA.
Based on my experience, ff02 AMBER polarised force field offers more
structural stability in simulations compared to non-polarised force field.
However, when it comes down to free energy calculations with MM-PBSA/GBSA,
calculations with non-polarised forcefields are more closely related to
experimental data whereas these calculations deviates more with polarised
versions. This could be attributed to lack of atomic radii and charge
parameters for explicit solvents with polarised forcefield and neglecting
the polarised energy, treatment of electrostatics in the MM-PBSA/GBSA
calculations.
Is there any development going on this field i.e. to incorporate or
parameterised MM/PBSA/GBSA with polarised force field FF02?
Your feedback is appreciated.
Cheers,
Neha Gandhi
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Received on Thu Oct 13 2011 - 23:00:02 PDT
