Re: [AMBER] problem with addIons in tleap

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 23 Jul 2011 13:45:40 -0700

The grid that I programmed extended much less than that from the solute,
maybe 6A. If that is still the case, the presence of ions outside the box
implies that one or more waters might be seen as solute. Were there any
waters in your loaded pdb file?


The minimal distance from the solute to the boundary was set to 15 A.
The dimensions of the water box are 157x150x128 A^3.
On Fri, Jul 22, 2011 at 1:51 PM, Bill Ross <> wrote:
>> After I solvated my protein, I used "addIons" to add ions to the
>> system to reach certain ion concentration. I found that some ions were
>> placed outside of the water box. Is this normal? When I used AMBER8
>> long time ago, this did not happen. I was wondering if this is
>> something with the new version of AmberTools.
> I wonder how big the water box is. Addions uses a grid based on
> a given distance from the solute, and a small box might fall
> within that distance.
> Bill
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Received on Sat Jul 23 2011 - 14:00:03 PDT
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