This is the mmpbsa.dat output file of my control ligand (ADP-ribose) using gmx_MMPBSA. However, the value of Bond energy seems a bit confusing to me? Don't energy values for molecular interaction usually remain in the range of thousands maximum? What does this absolutely colossal number mean...or why did it produce such a gigantic number? The UB and GGAS also exhibited similarly large numbers. Can anyone explain the probable reason to me?
GENERALIZED BORN:
Complex:
Energy Component Average SD(Prop.) SD SEM(Prop.)
-------------------------------------------------------------------------------
BOND 12279277.86 13355536.06 13355536.06 243837.61 243837.61
ANGLE 3541.77 2640.66 2640.66 48.21 48.21
DIHED 902.61 52.96 52.96 0.97 0.97
UB 1206251.57 1180528.38 1180528.38 21553.4 21553.4
IMP 905.41 1188.83 1188.83 21.71 21.71
CMAP -231.55 8.55 8.55 0.16 0.16
VDWAALS -1100.91 25.66 25.66 0.47 0.47
EEL -10446.72 144.22 144.22 2.63 2.63
4-VDW 390.51 10.44 10.44 0.19 0.19
4-EEL 8286.57 124.32 124.32 2.27 2.27
EGB -2048.84 130.02 130.02 2.37 2.37
ESURF 69.86 4.12 4.12 0.08 0.08
GGAS 13487777.11 13407609.75 14436276.29 244788.34 263569.14
GSOLV -1978.98 130.08 127.3 2.37 2.32
TOTAL 13485798.13 13407609.75 14436187.27 244788.34 263567.51
Hve you repeated the analysis??
Usually it should be in few thousands and total energy should be in the negative value for a better interaction......
Too much higher value might suggest the poor stability of that molecule at the binding pocket or absence of compound at the binding pocket..
Regards
Niaj Mohammad Tanvir It seems the trajectory is not fitted properly. PLease, check this section
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions
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