AMBER Archive (2002)

Subject: Magnesium as a DNA counterion in AMBER 6.0

From: Mike Keller (roguekel_at_yahoo.com)
Date: Thu Mar 28 2002 - 09:31:29 CST

Hello everyone,

I was curious if there was any trick to using Mg2+ as
a DNA counterion in AMBER. I've noticed that it isn't
a standard ion in this suite, though it is
parametrized in the Weiner et al force fields. I've
tried placing Mg2+ ions manually into my model,
loading the 91 parameter set in order to get the
proper available atoms types. It seemed like a
successful job in Xleap, but when I came to running a
simulation in Sander, it gives me the message, "Atom
type M is unknown." This confused me somewhat: I'd
manually designated the Mg ions as "MG" for all
necessary atom type fields.

Is there something I'm missing?

Thanks,

Mike Keller
UVA Chem dept.

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