Re: [AMBER] No solvent overlap

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 10 Jul 2010 10:29:24 -0700

> > It is odd that you are adding 12A of water before addIons, in
> > which case one would expect the ions to replace waters. I wonder
> > if the code has been changed.
> >
> And then: I am not sure if I understand you correctly. Is it odd to add
> the water first? What is the normal procedure? Or do you mean the fact
> that the ions don't replace water molecules?

Placing waters first turns on an option in addions whereby when
a grid point is chosen to place an ion, the nearest water is
replaced by the ion. I forget the width of the grid, but it
seems like 12A would be enough waters that there would always
be a near-enough one. Offhand I don't see how an ion would be
placed out of the box.

Although placing water first is recommended, you could try addions
first to see if it makes a difference - it should since the box is
drawn by solvation. If the ions are placed far from the solute,
you would likely want to add a smaller box clearance to avoid a
huge amount of waters. There is still something of a mystery here,
and I wonder if there's a bug in the code or the compiler.


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Received on Sat Jul 10 2010 - 10:30:06 PDT
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