AMBER Archive (2009)

Subject: Re: [AMBER] Understanding the all.out file in the MM-PBSA output

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Thu Mar 12 2009 - 05:54:27 CDT

Dear Xiaonan,

1) Regarding the relation of PBCAL and the "corrected reaction field energy" please have a look at:

http://archive.ambermd.org/200806/0227.html

2) PBSUR = "surface area" * SURFTEN + SURFOFF

Cheers!
Hannes Kopitz

University of Kiel
Germany

-------- Original-Nachricht --------
> Datum: Thu, 12 Mar 2009 09:39:10 +0800
> Von: "gmail" <heptoking_at_gmail.com>
> An: amber_at_ambermd.org
> Betreff: [AMBER] Understanding the all.out file in the MM-PBSA output

> Dear Amber users:
> The MM-PBSA module is a useful and convenient tool for binding free
> energy estimation. Most of the time, we are only interested in the
> statistics.out file in which the raw data in the all.out files have been
> processed.
> However, I find some problem in understanding the energy terms in the
> all.out files. Especially in the PBSA
> part.
>
> For example:
> this is part of complex.all.out file
> 1
> BOND = 567.9734 ANGLE = 1437.4321 DIHED =
> 1887.1406
> VDWAALS = -1483.4718 EEL = -13040.5101 EGB =
> -2288.8782
> 1-4 VDW = 647.3136 1-4 EEL = 7412.2126 RESTRAINT =
> 0.0000
> corrected reaction field energy: -3742.757259
> surface area = 9173.513
> ECAVITY = 9173.513
> EDISPER = 0.0000
>
> and this is the statistics.out file
>
> COMPLEX RECEPTOR LIGAND
>
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -5568.72 60.24 -5451.55 60.52 -76.46
> 1.34
> VDW -801.05 19.56 -744.16 19.14 7.41
> 2.22
> INT 3895.25 37.19 3802.19 36.23 93.06
> 6.04
> GAS -2474.52 72.66 -2393.52 71.95 24.01
> 5.94
> PBSUR 66.15 0.85 67.34 0.88 7.02
> 0.06
> PBCAL -2306.19 56.90 -2330.92 57.44 -39.45
> 0.80
> PBSOL -2240.05 56.53 -2263.58 57.09 -32.42
> 0.79
> PBELE -7874.91 21.07 -7782.47 21.34 -115.91
> 1.21
> PBTOT -4714.57 37.75 -4657.10 36.41 -8.41
> 5.79
> GBSUR 66.15 0.85 67.34 0.88 7.02
> 0.06
> GB -2353.39 59.16 -2367.57 59.10 -41.49
> 0.95
> GBSOL -2287.25 58.81 -2300.23 58.77 -34.47
> 0.93
> GBELE -7922.11 19.05 -7819.12 19.33 -117.96
> 1.21
> GBTOT -4761.76 36.98 -4693.75 35.94 -10.46
> 5.80
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -40.70 4.75
> VDW -64.31 3.63
> INT 0.00 0.00
> GAS -105.01 5.83
> PBSUR -8.22 0.37
> PBCAL 64.17 3.78
> PBSOL 55.95 3.65
> PBELE 23.47 3.74
> PBTOT -49.06 4.24
> GBSUR -8.22 0.37
> GB 55.67 3.71
> GBSOL 47.45 3.57
> GBELE 14.97 3.38
> GBTOT -57.56 3.95
>
> As I am quite unfamiliar with the equations in the PB and SA analyses,
> Could anyone kindly explain how to converse the corrected reaction field
> energy and surface area into PBCAL and PBSUR???
>
> Best Regards!
>
>
> Xiaonan Zhang
>
> Shanghai Public Health Clinical Center
>
>
>
>
> 

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