AMBER Archive (2006)

Subject: Re: AMBER: HBON in frcmod file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Oct 21 2006 - 03:24:42 CDT

Dear Bill,

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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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