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
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Received on Thu Apr 03 2014 - 13:00:02 PDT
