Re: [AMBER] How to deal with Heme?

From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
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.

Sincerely,

Anna CebriŠn

________________________________________
De: Abelak, Kavin <kabelak.rvc.ac.uk>
Enviat el: dimecres, 18 de maig de 2016 14:16:32
Per a: david.case.rutgers.edu; 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 (http://www.ncbi.nlm.nih.gov/pubmed/21997754); 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.

Regards,
Kavin

-----------------------------
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 <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> 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:

  http://sites.pharmacy.manchester.ac.uk/bryce/amber

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
this:

 NONBON
 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 - 08:00:04 PDT
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