AMBER Archive (2006)

Subject: AMBER: Decomposed GB energy in idecomp=3 option

From: Sukjoon Yoon (yoonsj_at_sookmyung.ac.kr)
Date: Mon Jan 30 2006 - 20:13:27 CST

Dear AMBER users and developers,

Energy decomposition was carried out with "idecomp=3" option. It
generated decomposed energies on a pairwise per-residue basis. An
example output is attached below. Polar and SAS part in GB were given at
each pairwise interaction energy. Could anybody explain to me what this
solvation energy terms mean in this (residue) pariwise interaction? How
was SAS calculated in such a residue-based interaction? In my
understanding, SAS is proportional to the surface area of the molecule.
I would also appreciate if anybody tell me what the pairwise "polar part
of the solvation energy" is ....

Thank you.

Sukjoon

                    PRINT PAIR DECOMP - TOTAL ENERGIES

    resid1 ->resid2 |internal |vdw |eel |pol |sas
======================================================================
TDC 1-> 1 0.000 -0.221 -39.490 -67.543 0.657
TDC 1-> 2 0.000 -0.822 -19.983 -0.424 -0.194
TDC 1-> 3 0.000 -0.537 -0.260 1.200 -0.111
TDC 1-> 4 0.000 -0.354 -1.350 1.087 -0.036
TDC 1-> 5 0.000 -0.027 -14.467 14.357 0.000
TDC 1-> 6 0.000 -0.008 -13.574 13.499 0.000
TDC 1-> 7 0.000 -0.001 0.674 -0.670 0.000
TDC 1-> 8 0.000 -0.002 0.556 -0.541 0.000
TDC 1-> 9 0.000 -0.006 0.263 -0.274 0.000
TDC 1-> 10 0.000 0.000 0.287 -0.286 0.000

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