AMBER Archive (2007)

Subject: AMBER: RE: about deoxy- and oxy- heme

From: Yang, Lee-Wei (lwy1_at_pitt.edu)
Date: Sun Oct 28 2007 - 02:52:58 CST


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_all.in Heme-his prep file, all atom
    frcmod.hemall Additional ff params, all atom
    heme_uni.in 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 (case_at_scripps.edu) 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 ---------------------------------------------------------------------------------

Lee
________________________________________
From: David A. Case [case_at_scripps.edu]
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, amber_at_scripps.edu,
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
http://amber.scripps.edu 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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