Re: [AMBER] differences in counterion position with water models and questions

From: Dr. Anselm Horn <>
Date: Mon, 10 May 2021 14:37:52 +0200

Dear Vaibhav,

I just want to comment to your question 2 very shortly: yes.

The difference in experimentally found micelle stability, which depended
on the nature of the counterion (Li+, Na+, K+), has been also
investigated computationally by MD and was called sodium effect (DOI
Our own investigations showed an influence of the nature of the
surrounding ions (Li+, Na+, K+) upon fibrillar amyloid-beta oligomers
(DOI 10.1007/s00894-018-3920-4), which is also known from experiment.
Of course, there might be more literature about that topic available.

In short, the different metal ions interacted in the simulations with
neighboring carboxylate groups in different ways, i.e. bridging vs.
non-bridging, which will in turn affected the stability of the overall
protein (complex).

Best regards,


On 05/07/2021 08:07 AM, Vaibhav Dixit wrote:
> Dear All,
> I am seeing some differences in the position of counterions with tleap that
> I think might have some impact on how conformations evolve during MD.
> This protein has an FMN co-factor.
> Following are the differences that I'm observing and some associated
> questions.
> Differences:
> 1) with ff14sb/tip3p, Na+ ions are placed away from the dianionic FMN
> phosphate group.
> 2) with ff19sb/opc, Na+ ions are placed close to FMN that form close
> contact during equilibration. This ion doesn't move away from FMN during a
> 40ns MD.
> 3) with ff19sb/opc, K+ ions are placed far away from FMN (may be due to
> large Van der Waals radii of K+).
> questions:
> 1) Since most exp. are done in KPi buffer to mimic intracellular
> conditions, why do many studies use Na+ ions for such proteins? Is it not
> better to always use K+ ions and avoid using Na+ (unless there are other
> reasons for using them)?
> 2) Can the differences in the choice of these counterions have a
> significant impact on the dynamics of the protein and complexes? (I think
> it may). There is some literature on ions vs. no ions (here
> <>and here
> <>), but I can't
> find comparisons between Na+ vs K+.
> 3) Is it possible to selectively include/exclude a region where counterions
> can be placed by tleap?
> 4) Is there a difference between the two commands "solvatebox mol opc 10"
> and solvatebox mol *opcbox *10"? the first did not give any error and
> simulations are running fine, but not sure if it is correct usage.
> Looking forward to valuable suggestions and tips from the list.
> thank you and best regards.
> Vaibhav

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Received on Mon May 10 2021 - 06:00:04 PDT
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