AMBER: RE: about deoxy- and oxy- heme

From: Yang, Lee-Wei <>
Date: Sun, 28 Oct 2007 04:52:58 -0400

Thanks very much Dr. Case. I will start with this paper you refered. I re-post the email I sent to you below in hope for other experts giving me advices.
(perhaps someone should replace your email address in the /home/software/amber/amber9_patch34/dat/contrib/heme/0README to the email address of the amber mailing list)

Best Regards,

------ the email to Dr Case regarding the oxy- and deoxy-heme ----------------
Dear Dr Case,

I'm studying the dynamics of Myoglobin (Mb) at the moment.

Can you forward me a few readings on how the force-field of heme is generated and why 'for historical reason', united atom force field is used for deoxy-state heme while all atom forcefield is used for oxy-state? Also, will these force field parameters reproduce the doming effect in Mb? I quote the oREADME text below. Thanks very much for your time on this.

" Heme-his prep file, all atom
    frcmod.hemall Additional ff params, all atom Heme-his prep file, united atom
    frcmod.hemuni Additional ff params, united atom

Use these carefully, since they are not part of the "standard"
AMBER distribution. Contact David Case ( if
you have questions about how these were generated. The heavy
atom names for the heme ring follow Brookhaven ideas, but the
protons are named according to a local, nmr-based convention.
For historical reasons, the united atom parameters are set up for
a deoxy heme, whereas the all-atom frcmod file is set up for a
ligated heme; you will want to carefully study these before
using them.
Best regards,
----- end ---------------------------------------------------------------------------------

From: David A. Case []
Sent: Friday, October 26, 2007 11:43 AM
To: Yang, Lee-Wei
Subject: Re: about deoxy- and oxy- heme

On Thu, Oct 25, 2007, Yang, Lee-Wei wrote:

> Dear Dr Case,

Please send amber-related questions to the mail reflector,,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar quesitons. See for information on how to subscribe.
> I'm studying the dynamics of Myoglobin (Mb) at the moment.

The heme files in the Amber distribution are very old, and might only be used
as a starting point. You probably should find more recent papers, such as the
one below, and start from there.

%A F. Autenrieth
%A E. Tajkhorshid
%A J. Baudry
%A Z. Luthey-Schulten
%T Classical Force Field Parameters for the Heme Prosthetic Group of
%Cytochrome c
%J J. Comput. Chem.
%V 25
%P 1613-1622
%D 2004

...good luck...dac

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Received on Wed Oct 31 2007 - 06:07:05 PDT
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