AMBER: Holding NA Base syn during annealing

From: Seth Lilavivat <>
Date: Thu, 22 Mar 2007 11:23:20 -0400

Dear Amber Users,

Any advice on trying to keep a NA base in the syn conformation (like Z-DNA)
while still being hydrogen bonded to its base pair during annealing? Right now
I'm starting with it in the syn conformation and have a torsion restraint of 90
to 270 degrees with a force constant of 200 kcal/mol. During the annealing run
it still pops back to the anti conformation.

Thanks in advance,

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Received on Sun Mar 25 2007 - 06:07:27 PDT
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