> I have to perform MD simulations for Haem containing protein, and I also
> want to account the charge effect during the dynamics. I am a bit confused
> during the use of forcefield for such type of simulations. Should I use
> polarizable forcefield such as ff02 otherwise ff12SB is sufficient? I
If I were to undertake a study, I would search for the most validated
protein force field and try to understand the limitations of each.
The Shahrokh heme parameters were built for the ff9X force fields; they
have not been tested or applied with the ff02/ff03 force field models
which use impose a different charge philosophy. It is not clear, at least
to my knowledge if you can mix and match the AMBER RESP ff9X charge model
with ff03 or ff02.
If you are trying to get a good polarizable force field for proteins, in
the context of a fixed charge model heme, good luck. I do not think there
is a clear "winner" or best model for polarizable treatment of proteins.
I would consider looking at the CHARMM Drude oscillator models, the AMOEBA
force field, etc, however definately in these cases you cannot graft a
fixed charge heme model on top; you would have to generate a compatible
model...
If you are going to apply the Shahrokh P450 heme model, it would be wise
to use one of the ff9X AMBER force fields, and likely the most recent. I
would think ff13 or ff14 (if it has been released).
--tec3
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Received on Wed Feb 26 2014 - 20:30:02 PST
