From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Nov 24 2016 - 14:41:58 CST
You might try with a non-bonded model, have a look at
On Dioxygen Permeation of MaL Laccase from the Thermophilic Fungus
*Melanocarpus
albomyces*: An all-Atom Molecular Dynamics Investigation (pages 1493–1501)
<http://onlinelibrary.wiley.com/doi/10.1002/cbdv.201600062/full>
Francesco Pietra
Version of Record online: Chemistry and Biodiversity 8 OCT 2016 | DOI:
10.1002/cbdv.201600062
Far easier than with a bonded model, however nothing can be plainly easy
with a complex system
best wishes
On Thu, Nov 24, 2016 at 9:01 PM, James Starlight <jmsstarlight_at_gmail.com>
wrote:
> Hi guys,
>
> yes, indeed, I am not a big expert in the simulations, like you have
> recognized!
> In fact, I am a MS molecular biologists whos major topic is fish
> distribution across the universe ocean!
> We have here some bioinformatics course which we have to pass to
> obtain money scholarships for the month.
> The things are tricky because my bioinformaticia teacher in fact is
> mad devil - he asked me to do this model in NAMD of multi-chain
> protein where each chain consist of several Cu2+ ions buried within
> internal cavities - and run short 10 ns simulation to check whether
> the model work or not. If I will not do it - he will not give his
> endorsement and I will not obtain money and have to skip black friday
> this year:(.
>
> I will be thankful for everyone who will demonstrate trivial way how
> to construct psf topology for this kind of model - assuming that I not
> need qm/mm in particular case, being motivated to sacrifice for the
> accuracy - parametrisation of the coordination bonds between
> active-site side chains and Cu2+, considering copper just like as
> non-bonded ion).
> It will helps me to give the fake model to the teacher to tell me
> "That's allright!" and sight the papper for my money!
>
>
> James S.
>
>
> 2016-11-24 1:52 GMT+04:00 Daniel Möller <daniel.moeller3_at_uni-greifswald.de
> >:
> > 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?
> >
> >
> >
> >
> >
> > Sincerely
> >
> >
> >
> > Daniel Möller
> >
> >
> >
> >
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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:
> > http://www.ks.uiuc.edu/~rcbernardi/QMMM/
> >
> >
> >
> > Best,
> >
> > Jerome
> >
> >
> >
> > On 23 November 2016 at 20:52, James Starlight <jmsstarlight_at_gmail.com>
> > 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!
> >
> > James
> >
> >
>
>
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