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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Received on Wed Feb 26 2014 - 14:30:03 PST
