[AMBER] problem in understanding the K+ parameter

From: Indrajit Deb <biky2004indra.gmail.com>
Date: Tue, 26 Aug 2014 18:04:54 +0530

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.

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)​

​But, In the original Dang's paper the value written as ---
(radius 3.332Å and well depth 0.1000 kcal/mol)​

​I am not getting why this difference.

Please explain me.



Indrajit Deb
Kolkata, India.
Mob: +919239202278
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Received on Tue Aug 26 2014 - 06:00:03 PDT
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