[gmx-users] Parametrization POM molecule

[Paolo Costa]

Dear Gromacs users,

I am new on Gromacs and in general on MD simulations.
I am interested on simulating a POM (polyoxometallate) molecule in a water
box.
I could already find in literature works dealing with POM:
- J. Phys. Chem. A 2005, 109, 1216-1222, Phys. Chem. Chem. Phys., 2008, 10,
6940–6953, J Comput Chem 32: 240–247, 2011, Chem. Eur. J. 2016, 22, 15280 –
15289.

By looking on those works, I could easily find the Lennard Jones parameters
for the non bonded interactions. *However, I could not find the parameters
for the bonded interactions.*
Do I need such parameters? In case, how can I find them? Because by looking
to this paper,  Chem. Eur. J. 2016, 22, 15280 – 15289, I will likely use
AMBER99 force field which it does not include any parameters for such
"exotic" molecule.

Thanks a lot.

Paolo
-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)