I generated a topology file of methane. And in that file the values of
ACOEFF and BCOEFF are as follows:
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
1.04308023E+06 9.71708117E+04 7.51607703E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
6.75612247E+02 1.26919150E+02 2.17257828E+01
Actually i want to know how these values came so, with parmed i got values
of LJ parameters which are as:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass
Charge GB Radius GB Screen
1 1 unk C1 C3 6 1.9080 0.1094
12.0100 -0.3884 1.7000 0.7200
2 1 unk H1 HC 1 1.4870 0.0157
1.0080 0.0971 1.3000 0.8500
3 1 unk H2 HC 1 1.4870 0.0157
1.0080 0.0971 1.3000 0.8500
4 1 unk H3 HC 1 1.4870 0.0157
1.0080 0.0971 1.3000 0.8500
5 1 unk H4 HC 1 1.4870 0.0157
1.0080 0.0971 1.3000 0.8500
and I think the units of lj radius(radius) are *kcal/mol* and of
epsilon(depth) is in *angstrom.*
after taking this i calculated the values of ACOEFF and BCOEFF and they
are as
>From prmtop Aij 1.04308023E+06 9.71708117E+04 7.51607703E+03
manually Aij 1018.6330 94.7933
7.3399
>From prmtop Bij 6.75612247E+02 1.26919150E+02 2.17257828E+01
manually Bij 0.6789
3.9620 21.1128
units Aij manually (kcal/mol angstrom^12)
units Bij manually (kcal/mol angstrom^6)
I want to know why they are not matching and what units are in A and B
which came from AMBER topology.
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Received on Thu Jul 16 2020 - 08:30:04 PDT
