AMBER Archive (2006)

Subject: Re: AMBER: improper torsion angle problem

From: David A. Case (
Date: Sun Sep 17 2006 - 18:52:38 CDT

On Wed, Sep 06, 2006, Fabian Alejandro Rodriguez wrote:
> 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?

It could well be that some NMR restraint is forcing a non-zero improper.
You could try removing (or reducing the force constants) for your restraints
to see what happens. You could also either change the force constant in the
force field, or add a pseudo NMR constraint to force the behavior you want.

...good luck...dac

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