From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Nov 24 2016 - 14:44:03 CST
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
>> >
>> >
>>
>
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