Re: ions behavior in protein-water box:

From: Emanuelle Bachelet (emanuellebachelet_at_gmail.com)
Date: Thu Oct 30 2008 - 12:24:27 CDT

Actually, one the Ca ions comes close to an aspartic acid - this is so not
good!

Well, one simulation I am trying now is to just fix the ions around their
equilibrated positions - (all these are more than 10A from any protein atom
after I finished equilibration). I will monitor the progress and if it
dosen't work I will introduce 9 sodium ions - I hope I won't have to make
the water box bigger to accomodate all of them.

I used Ca ions so I could keep the water box reasonable size and keep ions
at large distance from each other (instead of having 9 sodium ions since I
deleted the waters manually and put the ions in place of those 5 water
molecules). But i didn't think earlier that the Ca2+ will have such dramatic
effects.

Many thanks,
Ema.

On Wed, Oct 29, 2008 at 6:39 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> wrote:

> On Wed, 29 Oct 2008, Christopher Gillespie wrote:
>
> CG> Ema,
> CG>
> CG> I agree that the ions shouldn't effect the protein dramatically, but if
> you
> CG> are concerned with the interactions of the ions with the protein why
> include
> CG> the Ca2+ and not just Na+? If the protein is not restrained in any way
> the
> CG> ion effect over the length of the simulation should not be too
> dramatic.
> CG> Simple Brownian motion is going to move the ions with or without the
> CG> protein.
>
> to add to this: if you put a -9 charged object somewhere,
> it _is_ highly attactive to objects of the opposite charge,
> and doubly so for calciums. ;-)
>
> coulomb interactions are quite strong and range far, so
> i would not be too surprised to have some cations sticking
> rather closely to your protein. do you know for sure that
> there are none? how deeply are the anionic components buried?
>
> cheers,
> axel.
>
>
> CG>
> CG> Best,
> CG> Chris
> CG>
> CG>
> CG> On Oct 29, 2008, at 5:56 PM, Emanuelle Bachelet wrote:
> CG>
> CG> >Hi Chris,
> CG> >
> CG> >By closer I mean less than 5A, I haven't measured the exact distance
> CG> >because it's fluctuating. But imo, less than 5A means ions are going
> to
> CG> >modify the electrostatic interactions with/on the protein. Ions should
> be
> CG> >just to neutralize the system not to interact with the protein.
> CG> >
> CG> >I will also have a look at the reference you mention.
> CG> >
> CG> >Thanks,
> CG> >Ema
> CG> >
> CG> >On Wed, Oct 29, 2008 at 4:05 PM, Christopher Gillespie
> CG> ><gillescche_at_gmail.com> wrote:
> CG> >Ema,
> CG> >
> CG> >What exactly do you mean by "closer"? Ion association with protein
> CG> >surfaces is not necessarily an "incorrect" observation rather ions can
> CG> >interact with various parts routinely. Take a look at the work of
> Pavel
> CG> >Jungwirth on ion protein association.
> CG> >
> CG> >Best
> CG> >
> CG> >Chris
> CG> >
> CG> >
> CG> >
> CG> >On Oct 29, 2008, at 2:44 PM, Emanuelle Bachelet wrote:
> CG> >
> CG> >Hello,
> CG> >
> CG> >I have a question regarding ions in a simulation.
> CG> >
> CG> >I have a protein that has a net charge of -9 (it includes one of the
> CG> >residues which is phosphorylated). I immersed this protein in water
> box it
> CG> >and added 4 calcium ions and one sodium ion to neutralize the overall
> CG> >charge.
> CG> >
> CG> >But when my simulation system reaches .5ns of production dynamics
> (NVE),
> CG> >some ions move closer to the protein. In my opinion, they should not
> come
> CG> >too close to protein so as to modify the protein behavior. Does this
> mean
> CG> >that I constrain the ions at a particular position?
> CG> >
> CG> >thanks,
> CG> >Ema.
> CG> >
> CG> >
> CG>
> CG>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

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