Dear Mr. Swails,
Got it now.
Many thanks for you explanation.
---indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Tue, Aug 26, 2014 at 6:55 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, 2014-08-26 at 18:04 +0530, Indrajit Deb wrote:
> > Dear AMBER users,
> >
> > I am facing problem in understanding the K+ parameter.
> >
> > In the parm99.dat file, the default K+ parameter by Aqvist is as follows:
> >
> > K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021.
> > (adapted)
> >
> > I found people also using the Dang's parameter. As I found in the
> following
> > two papers the used the Dang's parameter for K+. There is report in
> mailing
> > list also.
> >
> > 1. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing
> > Nucleic Acids Force Fields. J. Chem. Theory Comput. 2009, 5, 2514–2530
> >
> > 2. Reference Simulations of Noncanonical Nucleic Acids with Different
> > χ Variants
> > of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J.
> > Chem. Theory Comput. 2012, 8, 2506−2520
> >
> > 3. http://archive.ambermd.org/201301/0367.html
> >
> > I found in all the above cases the parameter is as follows:
> > (radius 1.8687 Å and well depth of 0.100 kcal/mol)
>
> From what I could tell, the first paper you cited used a radius of
> 1.8700 A and a well depth of 0.100.
>
> > But, In the original Dang's paper the value written as ---
> > (radius 3.332Å and well depth 0.1000 kcal/mol)
>
> Not quite. The Dang parameters list sigma as 3.332. Sigma is not Rmin
> -- sigma is the distance at which the repulsive and attactive terms
> exactly cancel (i.e., the L-J potential is 0). Rmin, on the other hand,
> is the distance at which the potential energy function is a minimum
> (i.e., the lowest-energy distance). See
> http://eng.thesaurus.rusnano.com/upload/iblock/14c/lennard-jones%
> 20potential.jpg for clarification.
>
> The values in the Amber parameter files are actually Rmin/2, and Rmin is
> related to sigma via the equation:
>
> Rmin = sigma * 2^(1/6)
>
> So if you take Dang's sigma parameter, multiply it by the sixth root of
> 2, and divide that in half to convert to Rmin/2, then you get 1.8700 A.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Aug 26 2014 - 06:30:02 PDT
