[AMBER] metal site

From: Per Jr. Greisen <pgreisen.gmail.com>
Date: Mon, 2 Apr 2012 22:09:25 +0200

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 ) 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

all suggestions are more then welcome and needed


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Received on Mon Apr 02 2012 - 13:30:03 PDT
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