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intended for versions 4 and 5 and contain parameters which are apparently no
longer valid.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
Received on Thu Aug 01 2002 - 14:32:13 PDT
