AMBER Archive (2008)

Subject: Re: AMBER: QM/MM simulation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Nov 22 2008 - 08:53:50 CST

On Sat, Nov 22, 2008, Syed Tarique Moin wrote:
>
> I have developed a parameter for the active site of metalloprotein
> containing iron in its active site, now i am going to do a MD simulation for
> whole protein using this developed parameter. I want to know about the QM/MM
> simulation that i want to use this technique also. For QM/MM technique, Is
> force field for the metal site required to prepare the prmtop and inpcrd
> files for the further process i.e. QM/MM simulation using amber?
>

You *do* need a mm force field for the whole system, but the parameters for
the covalent part that will become QM can be dummy ones (if you like), since
they will not be used.

Note that Amber's QM/MM does not have any methods that support iron, so you
won't be able to do what you propose (without a lot of work).

...dac

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