Re: [AMBER] counterions placings

From: Jio M <>
Date: Fri, 9 Jul 2010 21:45:52 -0700 (PDT)

Dear Jason and Bill,

Thanks for reply

>and that should convince you that

>infinite distance is NOT the ideal location for ions according to this

>>See above - the leap code is also available.

I googled but didnt find.. can you please provide link if it is available.

"Calculating grid charges" actually why this is required still not able to get this.

Please correct me if I am wrong and help me to clarify (what I understood from tutorial;) :::: In grid, counterion will be placed, where least ESP is found. so charge (counterions) placed will be +1 or -1 in a grid  so why it needs to be calculated if it is a known value.

thanks and regards,


>At infinite distance, the system merely looks like a point charge with the
>charge of the net charge of the molecule, so there will be no electric field
>for a formally neutral protein.  However, that doesn't mean that the ESP is
>0 close to the protein where the point charge model is invalid.

If you want to take a look at the ESP, you can use a program like apbs or
some other PB solver.  VMD has an apbs plugin that will allow you to plot
and visualize the electrostatic potential, and that should convince you that
infinite distance is NOT the ideal location for ions according to this

Hope this helps,

> I am not able to understand meaning of "points of lowest/highest
> electrostatic potential" where counter charge is placed in

Highest/lowest is in the context of a set of points in grid
shape wrapped around the solute, maybe 10A wide (I forget
the exact dimension).

> 1) so does counterion is placed at farthest position always?

It turns out that since atomic charge is both negative and
positive within the solute, even with a net charge for the
whole solute, there can be local minima close in.

> 2) "Calculating grid charges" is displayed when addions is
> used..somebody please explain why this is required... or
> source from where I can know how calculations being done or
> atleast philosophical concept....

See above - the leap code is also available.
The initial points for the ions are somewhat arbitrary, as is
water placement; it is up to the user to equilibrate the ions
along with the water.


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Received on Fri Jul 09 2010 - 22:00:03 PDT
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