I am finding it nearly impossible to read your results. They are all
mangled on the same line. Please attach the results instead (and/or use an
email editor that doesn't do such horrible things to your text).
On Wed, Nov 11, 2015 at 6:11 AM, Hira Jabeen <hira_bioinfo.yahoo.com> wrote:
> 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 2.76Å and reaches the
> maximum value of 3.56Å. 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
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
> 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
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
> I request you to kindly guide me in resolving this problem.
> Regards,
> Hira Jabeen
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 11 2015 - 05:30:05 PST
