AMBER Archive (2003)

Subject: Re: AMBER: addions/xleap question

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Oct 01 2003 - 16:10:44 CDT

> I used the "addions" xleap command (from amber7) to neutralize a simple
> oligonucelotide-model. I checked the position of this Na+ ions after
> using this commands. I am quite surprised because they do NOT follow
> rigouroulsy the phosphate backbone: I would have expected that this
> each Na+ would be close to 'its' phosphate... Does it mean Na+ are
> more or less randomly added. It seems NOT the case if I read the
> description of the addions command in the amber7 documentation.

There are some bugs in the addions code. It is not clear whether
without these bugs you would see each ion directly on a phosphate,
since the algorithm places an ion then adds its contribution to
the grid before placing the next ion. Thus it is plausible that the
1st ion would be placed between two phosphates and things would go
downhill from there as far as matching ions to phosphates is
concerned.

The main thing, no matter what placement algorithm is used, is to
equilibrate. Once you equilibrate ions place by phosphates (as the
old Edit program did), you will see the ions in random-appearing
positions, typically with some ion pairs formed with pairs of waters.

Bill Ross

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