Re: [AMBER] amber topology file for cytochrome c covalently bond to Heme

From: David A Case <>
Date: Tue, 7 Jul 2015 11:27:42 -0600

On Mon, Jul 06, 2015, Shoresh Shafei wrote:
> I am trying to generate a topology file for pdb ID: 1c52 where
> histidine and methionine residues are covalently bond to Fe
> of the heme cofactor. The force field parameters provided
> by PhD thesis of Giammona has been used for cytochromes
> (

Sounds like you might want to use parameters for cytochromes (see below).
The Giammona parameters were for myoglobin-like proteins.

%A K. Shahrokh
%A A. Orendt
%A G.S. Yost
%A T.E. Cheatham, III
%T Quantum mechanically derived AMBER-compatible heme parameters for various
states of the cytochrome P450 catalyic cycle
%J J. Comput. Chem.
%V 33
%P 119-133
%D 2012

> When using this force field, I do not get any error, however there is no
> bond between Fe and NE2 of Histidine and Fe and S of Methionine.

You generally have to add the bonds to the protein residues manually in
tleap (using the "bond" command.) But see the paper cited above.

...good luck....dac

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Received on Tue Jul 07 2015 - 10:30:03 PDT
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