Dear Amber Users,
I would like to ask a question about energy decomposition. Why the surface
area term (using gbsa=2) are different for the same residue pair? For
example, in the following output, the surface term for 100->101 is -46.461
and that for 101->100 is -56.057. Which should be used to calculate the
interaction energy for the surface term? By the way, the last column lists
the solvent accessible surface areas.
Thanks a lot
Junmei
TDC 100-> 100 0.000 1.171 34.628 -68.445 299.479
TDC 100-> 101 0.000 0.107 -9.733 -2.069 -46.461
TDC 100-> 102 0.000 -0.772 0.280 -0.313 -31.130
TDC 100-> 103 0.000 -0.030 0.575 -0.670 0.000
TDC 100-> 104 0.000 -0.013 -0.325 0.337 0.000
TDC 100-> 105 0.000 -0.004 0.135 -0.114 0.000
TDC 100-> 106 0.000 -0.001 7.790 -7.689 0.000
TDC 100-> 107 0.000 -0.002 -0.111 0.101 0.000
TDC 100-> 108 0.000 0.000 0.084 -0.083 0.000
TDC 100-> 109 0.000 0.000 5.401 -5.334 0.000
TDC 100-> 110 0.000 0.000 5.697 -5.626 0.000
TDC 100-> 200 0.000 0.000 0.018 -0.018 0.000
TDC 100-> 201 0.000 0.000 -0.033 0.032 0.000
TDC 100-> 202 0.000 0.000 0.003 -0.002 0.000
TDC 100-> 203 0.000 0.000 -0.004 0.004 0.000
TDC 100-> 204 0.000 0.000 -0.043 0.043 0.000
TDC 100-> 205 0.000 0.000 -3.493 3.450 0.000
TDC 100-> 206 0.000 0.000 3.636 -3.590 0.000
TDC 100-> 207 0.000 0.000 -0.060 0.059 0.000
TDC 100-> 208 0.000 0.000 0.044 -0.043 0.000
TDC 100-> 209 0.000 0.000 0.073 -0.072 0.000
TDC 100-> 210 0.000 0.000 -0.080 0.079 0.000
TDC 101-> 100 0.000 0.107 -9.733 -2.069 -56.057
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Received on Tue Feb 14 2012 - 19:30:03 PST
