AMBER Archive (2006)

Subject: Re: AMBER: HBON in frcmod file

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Oct 21 2006 - 02:41:55 CDT

> I have a system which falls apart when implicit solvent is used. The
> system is composed of non-watson-crick bases; but it is experimentally
> shown that has a stable structure (and most probably a helical structure).

How did you equilibrate? Have you successfully equilibrated w-c bases?

Nucleic acids in general are sensitive in this regard.

Bill
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