Re: [AMBER] problem with addIons in tleap

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 22 Jul 2011 13:51:10 -0700

> 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.


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Received on Fri Jul 22 2011 - 14:00:05 PDT
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