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From: Jason Swails <jason.swails.gmail.com>

Date: Tue, 26 Aug 2014 09:25:33 -0400

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

Date: Tue, 26 Aug 2014 09:25:33 -0400

On Tue, 2014-08-26 at 18:04 +0530, Indrajit Deb wrote:

From what I could tell, the first paper you cited used a radius of

1.8700 A and a well depth of 0.100.

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Aug 26 2014 - 06:30:02 PDT

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