Dear Sir
I am getting high positive value for delta G due to positive Van Der Waal values while running MMPBSA for protein-ligand complex in AMBER12. The RMSD of the complex is stable with average value of 2.76 Å and reaches the maximum value of 3.56 Å. I also tried this in AMBER 14 with "indi=1" parameter in PB calculations but the results are same as below.
Here is the input file for AMBER12:
|Input file:|--------------------------------------------------------------|Input file for running PB and GB|&general| endframe=50, verbose=1,|# entropy=1,|/|&gb| igb=2, saltcon=0.100|/|&pb| inp=1, istrng=0.100, |/|--------------------------------------------------------------|MMPBSA.py Version=12.0|Solvated complex topology file: leub.prmtop|Complex topology file: cmpd.prmtop|Receptor topology file: un-leub.prmtop|Ligand topology file: UNK.prmtop|Initial mdcrd(s): leub_prod20.mdcrd||Receptor mask: ":1-348"|Ligand mask: ":349"|Ligand residue name is "UNK"||Calculations performed using 50 complex frames.|Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy||All units are reported in kcal/mole.--------------------------------------------------------------------------------------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -1962.2940 27.1613 3.8412EEL -23192.0383 51.0100 7.2139EGB -4869.3577 34.0766 4.8192ESURF 128.7914 0.9616 0.1360
G gas -25154.3323 52.7316 7.4574G solv -4740.5662 34.1573 4.8306
TOTAL -29894.8985 42.8850 6.0649
Receptor:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -2641.1798 20.4278 2.8889EEL -23144.4952 51.4037 7.2696EGB -4904.5695 35.1362 4.9690ESURF 132.6749 0.9466 0.1339
G gas -25785.6749 48.6163 6.8754G solv -4771.8946 35.1766 4.9747
TOTAL -30557.5695 34.6286 4.8972
Ligand:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -11.0295 1.0970 0.1551EEL -14.6132 1.9109 0.2702EGB -26.3144 1.2208 0.1726ESURF 5.2626 0.0541 0.0076
G gas -25.6427 2.1937 0.3102G solv -21.0518 1.2040 0.1703
TOTAL -46.6945 1.7108 0.2419
Differences (Complex - Receptor - Ligand):Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS 689.9152 23.4876 3.3216EEL -32.9299 4.7324 0.6693EGB 61.5262 3.6992 0.5231ESURF -9.1460 0.2385 0.0337
DELTA G gas 656.9854 24.4862 3.4629DELTA G solv 52.3802 3.6707 0.5191
DELTA TOTAL 709.3655 23.8033 3.3663
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POISSON BOLTZMANN:
Complex:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -1962.2940 27.1613 3.8412EEL -23192.0383 51.0100 7.2139EPB -4748.9914 36.0115 5.0928ENPOLAR 2711.9708 6.1314 0.8671EDISPER -1532.5199 7.3836 1.0442
G gas -25154.3323 52.7316 7.4574G solv -3569.5405 37.3620 5.2838
TOTAL -28723.8728 44.8599 6.3441
Receptor:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -2641.1798 20.4278 2.8889EEL -23144.4952 51.4037 7.2696EPB -4790.3762 37.6923 5.3305ENPOLAR 2697.7824 6.0474 0.8552EDISPER -1549.5715 7.3676 1.0419
G gas -25785.6749 48.6163 6.8754G solv -3642.1654 39.2689 5.5535
TOTAL -29427.8403 38.0709 5.3840
Ligand:Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS -11.0295 1.0970 0.1551EEL -14.6132 1.9109 0.2702EPB -28.6310 1.3386 0.1893ENPOLAR 62.0003 0.3656 0.0517EDISPER -64.7804 0.3628 0.0513
G gas -25.6427 2.1937 0.3102G solv -31.4111 1.3817 0.1954
TOTAL -57.0538 1.6614 0.2350
Differences (Complex - Receptor - Ligand):Energy Component Average Std. Dev. Std. Err. of Mean-------------------------------------------------------------------------------VDWAALS 689.9152 23.4876 3.3216EEL -32.9299 4.7324 0.6693EPB 70.0158 5.5994 0.7919ENPOLAR -47.8119 1.0197 0.1442EDISPER 81.8320 1.3137 0.1858
DELTA G gas 656.9854 24.4862 3.4629DELTA G solv 104.0360 6.2662 0.8862
DELTA TOTAL 761.0214 24.1782 3.4193
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I request you to kindly guide me in resolving this problem.
Regards,
Hira Jabeen
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Received on Wed Nov 11 2015 - 03:30:06 PST
