AMBER Archive (2006)

Subject: AMBER: MD of oligomer sequences

From: Atilio I Anzellotti/O/VCU (
Date: Thu Feb 02 2006 - 16:53:28 CST

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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