AMBER Archive (2008)

Subject: Re: AMBER: QM/MM simulation

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Sat Nov 22 2008 - 09:11:12 CST

Thanks David,

But do you think about SCF-DFTB support for Iron as mentioned in manual as implemented in amber10.

Regards

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com

--- On Sat, 11/22/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:

> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: AMBER: QM/MM simulation
> To: amber_at_scripps.edu
> Date: Saturday, November 22, 2008, 6:53 AM
> 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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