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From: Jio M <jiomm.yahoo.com>

Date: Sat, 10 Jul 2010 03:23:00 -0700 (PDT)

Thanks a lot again Sir

but one more thing:::

*>and the <"charge"> of the ion is 'added' to all the
*

*>remaining grid points. The process repeats until all ions are
*

*>added.
*

you mean to say potential instead of 'charge' here?

thanks and regards,

JIomm

--- On Sat, 7/10/10, Bill Ross <ross.cgl.ucsf.EDU> wrote:

From: Bill Ross <ross.cgl.ucsf.EDU>

Subject: Re: [AMBER] counterions placings

To: amber.ambermd.org

Date: Saturday, July 10, 2010, 5:45 AM

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

*>
*

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

If leap is available to you, then the source code should be also.

*> "Calculating grid charges" actually why this is required still
*

*> not able to get this.
*

The goal is to put, say, Na+ somewhere near a solute.

Since we do not have an analytical solution for calculating

the point of most negative potential, I devised a discrete

solution by marking the space with a grid. Once this is done,

the potential at each grid point is calculated by iterating

over each atom and accumulating the division of that atom's

charge by the distance to the point. Once all the grid points

have been calculated, the one with lowest potential is selected,

the Na+ is placed there, grid points enclosed by the ion are

deleted, and the charge of the ion is 'added' to all the

remaining grid points. The process repeats until all ions are

added.

*> 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.
*

The interesting value is the one before the ion is placed,

and what is interesting about it is that it is the greatest

or least of all the grid points.

Bill

*> > I am not able to understand meaning of "points of lowest/highest
*

*> > electrostatic potential" where counter charge is placed in
*

*> > http://ambermd.org/tutorials/basic/tutorial1/section2.htm
*

*>
*

*> 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 Sat Jul 10 2010 - 03:30:03 PDT

Date: Sat, 10 Jul 2010 03:23:00 -0700 (PDT)

Thanks a lot again Sir

but one more thing:::

you mean to say potential instead of 'charge' here?

thanks and regards,

JIomm

--- On Sat, 7/10/10, Bill Ross <ross.cgl.ucsf.EDU> wrote:

From: Bill Ross <ross.cgl.ucsf.EDU>

Subject: Re: [AMBER] counterions placings

To: amber.ambermd.org

Date: Saturday, July 10, 2010, 5:45 AM

If leap is available to you, then the source code should be also.

The goal is to put, say, Na+ somewhere near a solute.

Since we do not have an analytical solution for calculating

the point of most negative potential, I devised a discrete

solution by marking the space with a grid. Once this is done,

the potential at each grid point is calculated by iterating

over each atom and accumulating the division of that atom's

charge by the distance to the point. Once all the grid points

have been calculated, the one with lowest potential is selected,

the Na+ is placed there, grid points enclosed by the ion are

deleted, and the charge of the ion is 'added' to all the

remaining grid points. The process repeats until all ions are

added.

The interesting value is the one before the ion is placed,

and what is interesting about it is that it is the greatest

or least of all the grid points.

Bill

-----Inline Attachment Follows-----

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat Jul 10 2010 - 03:30:03 PDT

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