AW: Simulation of metalo-binding proteins

From: Daniel Möller (
Date: Wed Nov 23 2016 - 15:52:53 CST

Hi James,


for the AMBER-force field there are paper to describe a more correct way to handle of divalent ions. Here some example as a start:

1. Duarte, F.; Bauer, P.; Barrozo, A.; Amrein, B. A.; Purg, M.; Åqvist, J.; Kamerlin, S. C. L., Force Field Independent Metal Parameters Using a Nonbonded Dummy Model. The Journal of Physical Chemistry B 2014, 118 (16), 4351-4362, 10.1021/jp501737x.

2. Saxena, A.; García, A. E., Multisite Ion Model in Concentrated Solutions of Divalent Cations (MgCl2 and CaCl2): Osmotic Pressure Calculations. The Journal of Physical Chemistry B 2015, 119 (1), 219-227, 10.1021/jp507008x.

3. Saxena, A.; Sept, D., Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations. Journal of chemical theory and computation 2013, 9 (8), 3538-3542, 10.1021/ct400177g.


And I’ve a question to you: Are you new to molecular modelling/ dynamics or do you just want to expand your knowledge and expertise to a new field of proteins?





Daniel Möller




Von: [] Im Auftrag von Jérôme Hénin
Gesendet: Mittwoch, 23. November 2016 21:12
An: Namd Mailing List; James Starlight
Betreff: Re: namd-l: Simulation of metalo-binding proteins


Hi James,


To answer your question, allow me to start with this hypothetical request: "I wish to tighten a bolt using a hammer. Can you tell me the exact sequence of movements I need to do with my hammer to tighten this bolt?".


The answer, of course, is that you're looking at the wrong tool for the job. In short, the force fields implemented in NAMD suck at describing copper-protein interactions in any detail - which is what you want if you're interested in metal unbinding. There are special force fields for that, but they are more complex, and not implemented everywhere (see e.g. ligand field molecular mechanics).


Or you may want to look into QM/MM simulations:





On 23 November 2016 at 20:52, James Starlight <> wrote:

Dear NAMD users!

I would like to perform brute force MD simulation of some oligomeric
water-soluble protein, where each monomer has several Cu2+ ions buried
within the binding pockets. Could you suggest me some template of the
script used for the preparation and parametrizartion routine (which
force fields in better for the ions) of such big protein including
metalo-ions and some other tutorial which can be usefull in my case?
For the simplicity, I can consider in my model ions as the non-bound
model, assuming that I'm interesting to study of the escaping on the
metalo-ions during the long MD simulation.

Thanks for help!



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