Re: [AMBER] How to deal with Heme?

From: Abelak, Kavin <>
Date: Wed, 18 May 2016 12:16:32 +0000

Hi Morteza,

I’ve been doing some simulations on CYPs and using HEME parameters from Shahrokh et al 2012 (; The supplementary section has the penta-cordinate high spin as well as the dioxygen bound states for HEM, as well as the corresponding cys residues for the S-Fe bond.

You can email me if you need more info about setting up the molecule in tleap, etc - I’ve messed up enough times along the way to be able to diagnose any problems you will likely come across.


Kavin Abelak
PhD Student
Comparative Biomedical Sciences
Royal Veterinary College
4 Royal College St
London NW1 0TU

On 14 May 2016, at 14:16, David A Case <<>> wrote:

On Fri, May 13, 2016, Morteza Chehel Amirani wrote:

Just wondering where the old HEM parametrization files are located? It
seems they are removed from the current version i.e., 16.

They are at the contributed parameters database:

Unfortunately, frcmod.hemall file is missing two lines at the end, and I
haven't got the update posted yet. The frcmod.hemall file should end like

 FE 1.20000 0.05000 0.00000
 LO 1.60000 0.20000 0.00000
 LC 1.85 0.12 0.0
 NP 1.8240 0.1700 OPLS
 NO 1.8240 0.1700 OPLS

...good luck....dac

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Received on Wed May 18 2016 - 05:30:08 PDT
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