AMBER Archive (2002)

Subject: Zn/Mg Counterion placement around DNA

From: mdk7p_at_cms.mail.virginia.edu
Date: Fri Jun 28 2002 - 14:46:11 CDT

Hello everyone,

I'm trying to run MD calculations on DNA with Zn2+ and Mg2+
counterions, and I'm having trouble placing the ions properly. I know
that Addions doesn't handle divalent cations, and I thought that
placing them by hand and relaxing them via minimization would not work
nicely since I'm running with implicit solvent. Does anyone know of a
good method to place these ions around DNA?

Also, does anyone know of a good set of parameters for octahedral zinc
that could work with DNA?

Thanks!

Mike Keller
UVA Chemistry Dept.