Re: [AMBER] counterions placings

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 9 Jul 2010 10:11:02 -0700

> 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 - 10:30:04 PDT
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