[gmx-users] topology file for heme a3

[Aldo Jongejan]

Dear Jiancong,

You might have a look at the paper published by
Lopez and Kollman:

Lopez, M.A. and Kollman, P.A.; J. Am. Chem. Soc., 111 (1989), 6212-6222.

This is a heme c, but you could take it as a starting point.

I have parametrized a heme c for use in CVFF, much in the same
fashion as Laberge et al. published just before. My work on this
has been published in Prot. Engineering, 11 (1998), 185-198.

For CHARMM you might want to search for MacKerrel. There is,
as far as I know, no heme a3 topology available, but you can
start from the one available in CHARMM.

good luck,

aldo


Anton Feenstra wrote:
> 
> Jiancong Xu wrote:
> > Hi, guys,
> >
> > I apologize that this post is off subject a bit, but does anyone know how
> > to construct amber topology file for heme a3?
> >
> > Another question, is there any CHARMM topology file for heme a3 available?
> 
> You may want to (also) post this on the CCL...?
> 
> --
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
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> |  _   _  ___,| K. Anton Feenstra                                     |
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-- 
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NOTE: E-mail address has changed into

    jongejan at few.vu.nl

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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

e-mail: jongejan at few.vu.nl
tlf:    +31 (0)20 4447612
fax:    +31 (0)20 4447610

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