Re: [AMBER] Running QMMM on Iron Core enzyme

From: David A Case <>
Date: Mon, 11 Jun 2018 08:08:25 -0400

On Mon, Jun 11, 2018, Devashish_Das wrote:
> We are trying to run Methane Monoxygenase (MMO) QM/MM simulation with
> AMBER/GAMESS. MMO have diiron and forms a peculiar structure known as
> diamond core ([Fe2(μ-O)2]) for catalysis.
> We are going to run QMMM using AMBER/Gamess, so, metal centre still
> required to have amber parameters (obtained by Gamess)?

You are indeed required to have an MM description of the di-iron center,
but it doesn't have to be all that accurate, since the actual forces
will be determined by the QM part. Basically, you need good
Lennard-Jones parameters to prevent MM atoms from coming too close to QM

The rest of the MM force field can use any sort of rough estimate for
paramters. The fact that you are using Gamess has nothing to do with
how the MM force field is being used.

> Also, we have metal centre with residues around (as qm) but after running
> the gamess step, it shows the antechamber error, that it can't take
> multiple structure.

You can't use antechamber for metal centers, or (as you found out) for
more than one residue at a time. The program can help you
create parameters for iron centers.

....good luck....dac

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Received on Mon Jun 11 2018 - 05:30:04 PDT
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