AMBER Archive (2006)

Subject: Re: AMBER: HBON in frcmod file

From: Bill Ross (
Date: Sat Oct 21 2006 - 14:57:48 CDT


If it lasted 10 ns before falling apart, maybe it isn't a problem
with equilibration. I don't have any further advice except if it
stays together with explicit solvent, that is what I'd be inclined
to use :-)


> The system is a very small system; a tetramer. The structure is purely
> non-watson-crick base paired. It is (5-'iGiGiCiC-3')_2 helix, where iG and
> iC are isoGuanosine and isoCytidine, respectively. Because the system is
> small, I did not do any particular equilibration; namely, the initial and
> final temp.s were set to 300 K in the implicit solvent simulation. It fell
> apart after 10 ns. What happens is that the terminal base pairs opens up,
> and after that the structure fall apart. I did the same simulation to
> another tetramer which had 2 isoG-isoC and 2 G-C base pairs, and it didnt
> fall apart after 80 ns.
> I am thinking that the dipole moments of iG,iC have some effect on the
> structure, which might make the bases more polar compared to G and C. And
> as a result, it might lead the structure to fall apart.
> I did an explicit solvent simulation for this structure, and it was still
> helical after 60-70 ns; which make me think that the force field
> parameters are ok for this structure. Thanks in advance for your help.
> Best,
> On Sat, 21 Oct 2006, Bill Ross wrote:
> > > 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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