From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Fri Nov 25 2016 - 06:47:10 CST
Hi James,
You may find interesting this paper (it's open access), in which I dealt
with transition metal dications.
Copper2+ it's a rather particular case, you find comments in there but for
your purposes (non-bonded interactions) it should be fine.
http://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp00608f#!divAbstract
Cheers,
2016-11-24 21:44 GMT+01:00 James Starlight <jmsstarlight_at_gmail.com>:
> This is implemented in NAMD (I cant access to the paper right now)?
> If so, could you send me example of the script for the psfgen to make
> topology using bonded model for the ions?
>
> Thanks!
>
> James
>
> 2016-11-25 0:41 GMT+04:00 Francesco Pietra <chiendarret_at_gmail.com>:
> > 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)
> >
> > 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
> >> >
> >> >
> >>
> >
>
>
-- Luca Belmonte, PhD CIBIO - Center for Integrative Biology University of Trento Phone: +39 0461 28 27 91 Mobile: +39 328 45 81 762
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