Dear AMBER users,
I am modelling two DNA oligomers both 20 base pair long. One of them has
9 T-A base pairs and the other 11 T-A base pairs. According to
experimental data, the former should be more stable according to an
expected higher Tm point. The problem is that after 1.2 ns simulation the
energy of the former (9 T-A) is -61kcal while the other (11 T-A)
exhibited -65kcal which is the opposite to what I would expect, both
values for total energy are stable. I am using a WATBOX216 with 10.0.
Many Thanks for your feedback.
Atilio Anzellotti.
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Received on Fri Feb 03 2006 - 06:10:09 PST
