Hi Kshatresh,
If polarization plays a crucial role in your simulation than I would recommend using ff02 as it is a polarizable variant of ff99. ff12SB is a continuation of ff99SB with updated backbone and sidechain torsions and is not polarizable.
That said, I'm not sure if that system will model electron transfer or variations of charge distribution between the heme and protein because you are mixing a polarizable force field with QM derived static parameters. Try experimenting with the ff02+heme parameters to see if you get the desired effects.
Maybe someone else can weigh in on this?
Best,
Parker
-----Original Message-----
From: Kshatresh Dutta Dubey [mailto:kshatresh.gmail.com]
Sent: Wednesday, February 26, 2014 5:18 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Forcefield for transition metals
Dear Parker,
I am already using same parameters for haem provided in supplementary material of this article, so that is not problem. The problem is the use of suitable forcefield for surrounding protein as I am interested to account the effect of haem on protein and vice versa. Since for such systems, electron transfer and polarization plays a crucial role, therefore I am bit confused between the choice of suitable forcefield between ff12SB and ff02.
Thanks and regards
On Thu, Feb 27, 2014 at 12:05 AM, de Waal, Parker <Parker.DeWaal.vai.org>wrote:
> Hi Kshatresh,
>
> Because heme/haem groups are non-standard residues, and thus not
> parameterized within ff12SB or ff02, I would recommend looking into
> this set of QM derived heme parameters by Shahrokh et al.
> http://scanmail.trustwave.com/?c=129&d=mOiO0_-5ys6GZf-sNbvMGFMOs79cPzY
> MtYJ5B_Y9CQ&u=http%3a%2f%2fwww%2encbi%2enlm%2enih%2egov%2fpmc%2farticl
> es%2fPMC3242737%2f
>
> While these parameters were derived for P450s I'm sure one of the
> available states will suit your needs. You just need to decided which
> one most accurately represents your system.
>
> Alternatively if none of the states work for your system you could
> derive your own RESP charges via antechamber or use REDs for RESP
> charges and geometry optimization.
>
> I hope this helps.
>
> Cheers,
> Parker
>
> -----Original Message-----
> From: Kshatresh Dutta Dubey [mailto:kshatresh.gmail.com]
> Sent: Wednesday, February 26, 2014 4:40 PM
> To: AMBER Mailing List
> Subject: [AMBER] Forcefield for transition metals
>
> Dear Amber users,
>
> 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 will appreciate your suggestion in this regard.
> Thanks in advance.
> --
> 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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--
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 - 15:00:04 PST
