AMBER Archive (2007)

Subject: AMBER: Torsion Restraint on Glycosidic Bond

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Fri Feb 16 2007 - 15:13:52 CST

Dear Amber Users,

I am refining one of my models trying to hold a NA base in the syn conformation.
 I created an RST file and followed the protocol listed in the DNA tutorial. I
applied my restraint to a NA structure that I had already minimized and then ran
the annealing step. No matter what values I assign to the restraint, it doesn't
seem to affect the particular base that much. It still ends up in the normal
anti conformation. Am I going about this the right way?

Thanks,
Seth
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