Re: [AMBER] metal site

From: FyD <>
Date: Tue, 03 Apr 2012 12:01:20 +0200

Dear Per,

Did you follow the bonded and non-bonded energy values?
Is there any 'problem' with the 1-4 electrostatic term for instance?

regards, Francois

> I have some problems with a metal site I have parametrized in a protein. It
> is a copper site with four cysteine residue - so I start by doing a QM
> optimization of the geometry and getting a charge model using the
> Merz-Kollman in Turbomole. When I minimize with the newly added parameters
> the equilibrium distances and angles are reached - also during heating and
> for the first 20 ns of simulation but after 20 ns it starts to become
> strange two of the sulfur atoms come very close (~1.8 ) both are
> negatively charged and stays there furthermore the equilibrium distance is
> no longer sampled for the S-Cu distance it is shorten by 0.2 . The force
> constant for the metal-sulfur interaction is around 40 so it should be
> quite a penalty to the energy but mean and SD are the same.
> Clearly something is wrong but I have no idea how to narrow it down - I
> have create the residues using templates from library files of e.g. CYM and
> HIE and the generated frcmod file with the missing parameters. I have added
> a new atom type for the sulfur but is added as atom type "S" "sp3". I have
> check the prmtop and it contains the force constants etc. Also in the leap
> log I do not see any errors or warnings related to the metal site and its
> residues.
> all suggestions are more then welcome and needed

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Received on Tue Apr 03 2012 - 03:30:03 PDT
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