ZN ions
Dear CCLrs I am trying to simulate a ZN peptidase. The problem is that
the ZN ion, which is directed by an anterior sulphur atom to donate
certain orbitals to one carboxylate oxygen and one carbonyl oxygen for
polarization effect to carry out catalysis, is presented in the
GROMOS96
force fields as a structural ion. Indeed, you could say that I am
expecting an EVB/QM model of the ZN ion in a MD program, however I was
thinking it could be possible to reduce the current hexacoordinated
state to tetra coordinated state somehow.
I have been advised to create a topology of the tetra coordinated state
manually, but this is rather tedious because of the state of the
protein-inhibitor complex.
Are there options to modify the parameters in the GROMOS force field
to
your knowledge?
Sergio