AMBER Archive (2006)

Subject: Re: AMBER: DNA tutorial xleap help

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Feb 08 2006 - 13:56:25 CST

> I can see the ions were added in a straight line along
> the bottom, perpendicular to the DNA helix. This also messes up the next
> solvation step.

If you solvate first, then addIons, you will may get a
better result.

> It is a machine-dependent bug,

Not entirely - there are a few known bugs in addIons, and the
extreme sort of case you are seeing is apparently a machine-
dependant manifestation.

Bill
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