AMBER Archive (2002)

Subject: Solvated DNA using Amber 7

From: Nicholson, James D Mr ARO (James.Nicholson_at_apg.amedd.army.mil)
Date: Thu Aug 01 2002 - 16:32:13 CDT

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intended for versions 4 and 5 and contain parameters which are apparently no
longer valid.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
calculation?

-Jim Nicholson