Re: [AMBER] How to deal with Heme?

From: Anna Cebrian Prats <>
Date: Wed, 18 May 2016 14:32:59 +0000

Hi Kavin,

I already working with the Ferric (IV) hexa-coordinate compound I protoporphyrin with His residue for the NE2-Fe bond and Fe-O bond.

I am also following the HEME parameters from Shahrok et al 2012 supplementary section material.
However, I have some troubles

I want to use the HEM.mol2 file of (compound I hexa-coordinate) to use the charges but the Cartesian coordinate not coincide then I have to create a new .mol2 file with my coordinate and take the charges from the Shahrok file, haven't I? Who can obtain a .mol2 file?

A part from that, I create with antechamber a .mol2 file only for the histidine residue.

With regard to .frcmod file I am using the CPDI.frcmod but without the parameters corresponding to CYs, is right?

Then I use the tleap with this input;

> source leaprc.ff14SB
> source leaprc.graff
> loadambparams *.frcmod
> loadmol2 HIS.mol2
> loadmol2 HEM.mol2
> x = loadpdb allsystem.pdb ( how can obtain the pdb of the all system, using cat HEM.mol2 HIS.mol2 > allsystem.pdb ? )

Then i obtain this message :
Unknown residue: HEM number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: HEM sequence: 555
create a new atom name with all the atoms of HEM group.

What I am doing wrong? Can you help me or guide me a little bit please.

Thank you in advanced for your help.


Anna CebriŠn

De: Abelak, Kavin <>
Enviat el: dimecres, 18 de maig de 2016 14:16:32
Per a:; AMBER Mailing List
Tema: Re: [AMBER] How to deal with Heme?

Hi Morteza,

Iíve 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 - Iíve 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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