Re: AMBER: DNA tutorial xleap help

From: Bill Ross <>
Date: Wed, 8 Feb 2006 11:56:25 -0800 (PST)

> 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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Feb 12 2006 - 06:10:05 PST
Custom Search