Dear Matias and Amber list
I will read these soon.
I'm additionally wondering if the K+ ions enter protein active sites
especially when the entry-exist channels are available and K has auxillary
or noncatalytic roles?
My first impression is that K+ doesn't appear with reasonable frequencies
in pdb database in the active sites for these two types. But is it likely
to be a experimental artifact or more real representative of the facts?
Please let me know your thoughts on this
Thanks and best regards.
Vaibhav
On Fri, Mar 6, 2020, 21:03 Matias Machado <mmachado.pasteur.edu.uy> wrote:
> just a correction: "As we proved for SLTCAP,..." => "As we proved for
> SPLIT,..."
>
> :-P
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Viernes, 6 de Marzo 2020 12:29:54
> Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear Vaibhav,
>
> Dealing with polyvalent salts (e.g. CaCl2) and complex mixtures is not a
> trivial issue...
>
> The "rule" of just dividing by N is wrong as the charge of each ionic
> specie must be considered to preserve the electroneutrality of the system.
>
> For that, Salinator utility of CHARMM-GUI uses a more general expression
> of SPLIT:
>
> N+ = No - Q/(2*Z+)
> N- = Z+*No + Q/2
>
> where Z+ is the charge of the cation, see [
> http://www.charmm-gui.org/?doc=input/solution][https://doi.org/10.1002/jcc.20945
> ].
>
> But be aware that its application range wasn't validated, as we did in
> SPLIT. Indeed, the following authors' recommendation may be wrong:
>
> "In the case that the number of an ion type becomes negative due to highly
> charged biomolecular systems such as DNA or RNA, Solvator displays a
> warning and asks users to increase the concentration." [
> https://doi.org/10.1002/jcc.20945].
>
> As we proved for SLTCAP, there is a clear cutoff (No/Q<1) at which
> deviations from SLTCAP are unacceptable (i.e the linearized
> Poisson‐Boltzmann assumption is not valid in that range). A similar rule
> should be set for the general expression.
>
> Notice that former approximations are for one ion pair in the solution...
> to deal with complex salt mixtures (NaCl + KCl + CaCl2 + ...) you have to
> take into account the ionic strength of the solution... so adding (let say)
> 4 Ca2+ ions is different than adding 8 Na+ ions, despite the net charge is
> the same...
>
> At the moment I don't know of any simple and general rule to tackle all
> these issues at the same time...
>
> Alternative, you could try using a semigrand canonical osmostat [
> https://doi.org/10.1021/acs.jpcb.7b11734]. Despite being more accurate,
> in my experience it may be ~30 times slower than a regular NVT/NPT
> simulation.
>
> Hope this helps...
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Jueves, 5 de Marzo 2020 1:19:41
> Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear Matias and Amber list,
> Thanks for the interesting suggestions and reference (I'll read it in
> detail soon).
> Just wondering if one can generalize this to dividing the charge by n,
> where n is the total number of unique ions.
> E.g. divide by 3 in case we want a combination of NaCl (2.5 mM) and KCl
> (140 mM) at their typical intracellular concentrations.
> Using this one can then simulate situations where intracellular Ca ions
> increases 10-1000 fold (here we will divide by 5 to account for NaCl, KCl
> and CaCl2).
>
> Please let me know your thoughts and if this approach is meaningful.
> Thank you.
>
> On Thu, Mar 5, 2020 at 5:55 AM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > you can also check this previous post:
> >
> > [http://archive.ambermd.org/202002/0194.html]
> >
> > Best,
> >
> > Matias
> >
> > ----- Mensaje original -----
> > De: "Matias Machado" <mmachado.pasteur.edu.uy>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Miércoles, 4 de Marzo 2020 21:23:01
> > Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
> >
> > Dear Vaibhav,
> >
> > I recommend you to use the SPLIT method, which is described here:
> >
> > Split the Charge Difference in Two! A Rule of Thumb for Adding Proper
> > Amounts of Ions in MD Simulations
> > [https://doi.org/10.1021/acs.jctc.9b00953]
> >
> > The keyword "saltcon" has nothing to do in explicit solvent MDs.
> >
> > Best regards,
> >
> > Matias Machado
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Miércoles, 4 de Marzo 2020 9:49:40
> > Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc
> >
> > Dear All,
> > I'm interested in understanding if/which Na, K and Cl ions explicitly
> enter
> > into the active site of a given protein during MD simulation.
> > But I can't find a way/trick (from the manual or older posts) to add all
> > these ions matching the intracellular concentrations and while keeping
> the
> > system neutral.
> > I'm guessing someone in the list must have already done a similar thing.
> > Thus can someone please suggest me on this aspect.
> > I'm assuming that if this can be done then I'll have to use saltcon=0 to
> > avoid GB modelling for salt concentrations.
> > Looking forward to receiving valuable suggestions from the list.
> >
> > Thank you and best regards.
> > Vaibhav
> >
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> The
> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
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>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
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Received on Fri Mar 06 2020 - 08:00:03 PST
