Re: [AMBER] metal site

From: Jason Swails <>
Date: Mon, 2 Apr 2012 23:51:34 -0400

On Apr 2, 2012, at 4:09 PM, "Per Jr. Greisen" <> wrote:

> Hi all,
> 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 Å) both are

Are the sulfur atoms all bonded directly to the metal? If so, there are no nonbonded interactions calculated between the sulfurs since they create an angle (likewise there are no nonbonded interactions calculated between bonded atoms).

In this case, it's the more angle force constant that controls the S-S distance.


> negatively charged and stays there furthermore the equilibrium distance is
> no longer sampled for the S-Cu distance it is shorten by 0.2 Å. 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
> thanks
> --
> Per
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Apr 02 2012 - 21:00:03 PDT
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