[AMBER] Parameters for Ca+2 ion for the decomposition analysis

From: Manikanthan Bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Thu, 3 Apr 2014 15:22:01 -0400

Dear All,

I want to incorporate the parameters for the Ca+2 ion in the
$AMBERHOME/src/sander/mdread.F90 file. The radius of Ca+2 ion is about
1.3264 angstrom as given in the following link:

http://ambermd.org/Questions/vdw.html

I have noticed that in the mdread.F90 contains the parameters for Mg+2 ion


 else if (atype == 'MG') then
               ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107,
5422
               ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107,
5422
               ! Mg radius = 1.45A: Aqvist 1992
               x(l165-1+i) = 1.18d0 + 1.4d0
               ! The following values were taken from O.sp3 with two
bonded
               ! neighbors -> O has the smallest van der Waals radius
               ! compared to all other elements which had been parametrized
               x(l170-1+i) = 0.49392d0
               x(l175-1+i) = -0.16038d0
               x(l180-1+i) = -0.00015512d0
               x(l185-1+i) = 0.00016453d0

How to define the highlighted parameters for a Ca+2 ion? Can anybody
explain me what these numbers mean?

mani 




-- 
Manikanthan Bhavaraju
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Received on Thu Apr 03 2014 - 12:30:03 PDT
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