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
