AMBER Archive (2003)

Subject: Re: AMBER: Reference for Amber7 heme parameters

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 08 2003 - 10:23:46 CDT

On Fri, Aug 08, 2003, Ross Walker wrote:

> I am looking for a reference for the heme parameters provided with Amber
> 7 in ./dat/contrib/heme.
>
> The frcmod.hemall file lists the following in the header:
>
> Force field parameters were adapted from D.A. Giammona, Ph.D. thesis,
> University of California, Davis (1984).
>
> Does anyone know if this is the only reference for these parameters or
> are they published elsewhere?

They were never published elsewhere. Several other groups have come up
with force field parameters for hemes; it would be a real benefit to the
community (given the common occurrence of heme proteins) for someone to
assemble these references and at least document the various choices one has.
Papers from the Spiro and Shelnutt/Woody groups would a good place to start.
A lot has been learned about hemes and heme deformations since 1984.

If someone wants to seriously look at this, I could provide a copy of the
relevant portions of Ann's thesis.

..regards....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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