AMBER Archive (2009)

Subject: RE: [AMBER] How to denature DNA

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Sep 09 2009 - 12:14:37 CDT

Dear Dr. Bill ,

Thank you for the explanation ,
I will read the paper ,
I will post my doubts after i start doing simulation ,

if you find more details could you please let me know

regards
balaji

> Date: Wed, 9 Sep 2009 09:38:04 -0700
> From: ross_at_cgl.ucsf.edu
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] How to denature DNA
>
> > Dear Dr. Bill =2C=20
> >
> > Sorry =2C I can not understand .=20
> > could you suggest me some reference =2C or=20
> > can I have more explanation .=20
>
> The manual is the reference for how to construct flat-well
> distance restraints. I'm not sure exactly how one would calculate
> the free energy of dissociation, except that it might involve
> gradually increasing the distance restraint in multiple dynamics
> runs and combining the distance distributions from each run
> somehow; I'm not sure whether Amber provides tools for the
> combining part.
>
> I would read the manual carefully and look for papers about
> similar calculations. It is unclear whether there is enough time
> to make a good calc of this problem. If you can get the tools
> together, I would try a short strand first, maybe 5 base pairs.
>
> A long time ago I tackled this problem with different software:
>
> DNA Dynamics in Aqueous Solution: Opening the Double Helix.
> A. Pohorille, W.S. Ross, and I. Tinoco, Jr.
> International Journal of Supercomputing Applications 4:3, 81
> (1990).
>
> Bill
>
>
> >
> > thanking you=20
> >
> > regards=20
> > balaji
> >
> >
> > > Date: Tue=2C 8 Sep 2009 10:33:09 -0700
> > > From: ross_at_cgl.ucsf.edu
> > > To: amber_at_ambermd.org
> > > Subject: RE: [AMBER] How to denature DNA
> > >=20
> > > > Is it possible to do with amber=20
> > >=20
> > > You can use restraints to force an increasing distance between pairs
> > > of atoms. Measuring free energy of dissociation probably takes more
> > > work to set up and calculate.
> > >=20
> > > Bill
> > >=20
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