Dear AMBERusersanddevelopers,
IhaveusedMM_PBSA/GBSAmethod for calculatingfreeenergyinsomecases.InAMBER16manual,
the mm_pbsa output is explained as following:
*** Abbreviations for mm_pbsa output ***
ELE - non-bonded electrostatic energy + 1,4-electrostatic energy
VDW - non-bonded van der Waals energy + 1,4-van der Waals energy
INT - bond, angle, dihedral energies
GAS - ELE + VDW + INT
PBSUR - hydrophobic contrib. to solv. free energy for PB calculations
PBCAL - reaction field energy calculated by PB
PBSOL - PBSUR + PBCAL
PBELE - PBCAL + ELE
PBTOT - PBSOL + GAS
GBSUR - hydrophobic contrib. to solv. free energy for GB calculations
GB - reaction field energy calculated by GB
GBSOL - GBSUR + GB
GBELE - GB + ELE
GBTOT - GBSOL + GAS
TSTRA - translational entropy (as calculated by nmode) times temperature
TSROT - rotational entropy (as calculated by nmode) times temperature
TSVIB - vibrational entropy (as calculated by nmode) times temperature
*** Prefixes in front of abbreviations for energy decomposition ***
"T" - energy part due to _T_otal residue
"S" - energy part due to _S_idechain atoms
"B" - energy part due to _B_ackbone atoms
However,IfindsomequestionswhenIcheckthedata.The formula PBSOL = PBSUR + PBCAL is not ture in my data.
SO I go to $AMBERHOME/src/mm_pbsa/Examples directory to see examples's data,and find the formula PBSOL = PBSUR + PBCAL
is also not ture.The following is the examples's data:
The file in my linux: amber16/AmberTools/src/mm_pbsa/Examples/03_MMPBSA_Binding/test_statistics.out.save
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7615.10 14.32 -3510.91 27.05 -3289.01 11.56
VDW -1024.18 11.86 -451.18 6.70 -493.12 3.46
INT 5896.62 59.36 3071.10 38.75 2825.52 33.81
GAS -2742.67 61.81 -890.98 44.15 -956.61 42.72
PBSUR 2224.78 8.90 1174.44 3.46 1116.88 6.67
PBCAL -3410.74 9.85 -2148.21 16.71 -2081.63 4.31
PBSOL -2553.13 6.69 -1716.80 14.90 -1718.39 3.37
PBELE -11025.84 4.47 -5659.12 10.66 -5370.64 7.33
PBTOT -5295.80 56.96 -2607.78 34.89 -2675.00 40.17
GBSUR 80.01 0.55 46.74 0.13 42.76 0.63
GB -3793.83 24.79 -2345.81 22.00 -2265.27 13.47
GBSOL -3713.83 24.32 -2299.07 21.92 -2222.51 13.17
GBELE -11408.94 10.64 -5856.72 14.41 -5554.28 4.87
GBTOT -6456.50 40.25 -3190.05 23.57 -3179.12 30.96
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -815.19 26.53
VDW -79.89 8.36
INT 0.00 0.00
GAS -895.07 18.81
PBSUR -66.53 1.29
PBCAL 819.11 19.36
PBSOL 882.06 17.99
PBELE 3.92 7.18
PBTOT -13.02 4.06
GBSUR -9.49 0.20
GB 817.24 23.53
GBSOL 807.75 23.65
GBELE 2.05 3.13
GBTOT -87.32 6.05
So the phenomenon lead to the PBTOT is wrong, becuase PBTOT = PBSOL + GAS. I want to know
how to explaine this phenmenon and deal with it ?
Thank you in advance.
Qiankun Gong
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Received on Tue Jul 10 2018 - 05:00:02 PDT
