AMBER Archive (2006)

Subject: AMBER: improper torsion angle problem

From: Fabian Alejandro Rodriguez (
Date: Wed Sep 06 2006 - 16:52:40 CDT

Hello everybody,

I ran my restrained MD and I satisfied all my NMR restrains that I had,
but I realise checking my sample that the improper angle between (in
DNA) a base and its own sugar ring it's not zero. I mean, the improper
angle C8-C1'-N9-C4 is not zero. For some bases this angle is zero and
for others it is not.
Do you have any idea why this happened? Is there any way to force this
angle to be zero? Is it because I have a wrong NMR restraint that force
this angle be different from zero?

Thank you in advance for your help.

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