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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242737/
>
> 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 - 14:30:05 PST
