Solvated DNA using Amber 7

From: Nicholson, James D Mr ARO <>
Date: Thu 1 Aug 2002 17:32:13 -0400

I'm running solved B-form DNA using sander in the Amber 7 package. There
are some fairly significant deviations from B-form.

I'm following the protocol as described in Cheatham, Cieplak, Kollman (J.
Biomolec. Struct. & Dyn., 16(4), 1999) and also in Konerding, Cheatham,
Kollman, James (J. Biomolec. NMR). The input files I've found are really
intended for versions 4 and 5 and contain parameters which are apparently no
longer valid.

Can anyone advise me on the viability of sander v.6 & 7 for this

-Jim Nicholson
Received on Thu Aug 01 2002 - 14:32:13 PDT
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