AMBER Archive (2007)

Subject: AMBER: Holding NA Base syn during annealing

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Mar 22 2007 - 09:23:20 CST

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,
Seth 

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