AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Feb 16 2006 - 12:49:20 CST

> > Alternative way is to take the i-tetraplex, to remove
> > one of its self-intercalated duplexes, and let the rest
> > relaxe as duplex via MD.
> I've done such two test 100ps simulations with implisit solvent
> starting from the modified 190d.pdb with and without weak positional

I would be hesitant to use implicit water when dealing with
speculative models. Perhaps others could comment..

Bill
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