AMBER Archive (2009)

Subject: RE: [AMBER] How to denature DNA

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 09 2009 - 11:38:04 CDT

> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _________________________________________________________________
> Sports=2C news=2C fashion and entertainment. Pick it all up in a package ca=
> lled MSN India
> http://in.msn.com=
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber