AMBER Archive (2009)

Subject: Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter

From: FyD (
Date: Thu Sep 03 2009 - 02:03:45 CDT

Dear Haining Lu,

> I want to run a MD simulation on hemoglobin. My question is how to get
> the parameter for heme? From a literature search, people seem to
> consider the (heme + O2 + Fe(II) + histidine) as a whole residue and
> calculate the RESP charge using the Gaussian program.

I think you should condider all the ligands connected to the Fe(II) &
not only the porphyrin ring...

> However, if such
> a system is used in Gaussian, the histidine residue is not complete,
> i.e., its backbone is cut from crystal structure. In that case, how can
> I determine the total charge of the system in order to run the quantum
> calculation? The second question is how to let the AMBER program know
> that the histdine should be included in heme? Do I have to modify the
> PDB file?

Here, the idea is to generate a molecular fragment (i.e. a new force
field library) for your heme system. Your case is a little complex but
you will find many examples of generation of basic molecular fragments
@ The presence of the metal
atom makes the system more complex (mainly in QM & during fitting
step) but does not change the strategy for building a molecular
fragment. You build such a molecular fragment from a whole molecule
from which some atoms are removed. The group of atoms which is removed
is usually constrained during the charge fit (using the RESP program).

At the end, the fragment built has to be compatible with the other FF
libraries (belonging to the FF you chose) used to construct/recognize
the entire biopolymer (containing the metal complex).

Finally, to answer to "how to let the AMBER program know that the
histdine", the LEaP program is used for automatic recognition between
the PDB file (biopolymer with the metal complex) and the FF libraries
required: this recognition is simply based on residue & atom names. If
a perfect match between the residue & atom names found in the PDB file
& these in the FF libraries previously loaded occurs, you will be able
generate the prmtop/prmcrd files for MD simulation.

These are only generalities & will not help that much.
May be, you could first read the tutorials @
and then come back with more specific questions regarding how to built
your metal complex fragment.

regards, Francois

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