Dear Prof Cheatham and Parker,
Thanks for detail explanations.
On Thu, Feb 27, 2014 at 5:57 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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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--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Wed Feb 26 2014 - 22:00:03 PST
