I just sent an answer to what was, in effect, the exact same question just
a minute ago.
The reason MMPBSA.py gives different PB values is a different nonpolar
solvation free energy model. Try putting inp=1 in the &pb section and
rerun the calculations. Agreement with tutorial results should be much
better.
HTH,
Jason
On Mon, Oct 19, 2015 at 10:58 AM, MarcZhang <progress0935zhang.gmail.com>
wrote:
> Dear Amber user group
>
>
>
> I found differences on my MMPBSA calculation results, when I tried to
> reproduce the results in the Amber tutorial.
>
>
>
> The binding free energy of Ras-Raf was calculated using the exact input
> files and trajectory files from the tutorial. (AMBER ADVANCED TUTORIALS
> TUTORIAL 3 - SECTION 3.1)
>
>
>
> The calculation results suggested that MMGBSA returned decent values but
> results of MMPBSA were far deviated from the values given in the tutorial.
>
>
>
> The only differences I found in the results file is that my calculation
> used
> mmpbsa_py_energy PBSA solver instead of sander in tutorial.
>
>
>
> Is this the reason for the deviations? How can I change the solver, if it
> is
> cause.
>
>
>
> Thank you very much for your help!
>
>
>
> Cheers
>
>
>
>
>
> Here is the my calculation results:
>
> | Run on Mon Oct 19 14:16:21 2015
>
> |
>
> |Input file:
>
> |--------------------------------------------------------------
>
> |Input file for running PB and GB
>
> |&general
>
> | endframe=50, verbose=1,
>
> |# entropy=1,
>
> |/
>
> |&gb
>
> | igb=2, saltcon=0.100
>
> |/
>
> |&pb
>
> | istrng=0.100,
>
> |/
>
> |--------------------------------------------------------------
>
> |MMPBSA.py Version=13.0
>
> |Solvated complex topology file: ras-raf_solvated.prmtop
>
> |Complex topology file: ras-raf.prmtop
>
> |Receptor topology file: ras.prmtop
>
> |Ligand topology file: raf.prmtop
>
> |Initial mdcrd(s): prod.mdcrd
>
> |
>
> |Receptor mask: ":1-166"
>
> |Ligand mask: ":167-242"
>
> |
>
> |Calculations performed using 50 complex frames.
>
> |Poisson Boltzmann calculations performed using internal PBSA solver in
> mmpbsa_py_energy
>
> |
>
> |Generalized Born ESURF calculated using 'LCPO' surface areas
>
> |
>
> |All units are reported in kcal/mole.
>
>
> ----------------------------------------------------------------------------
> ---
>
>
> ----------------------------------------------------------------------------
> ---
>
>
>
> GENERALIZED BORN:
>
>
>
> Complex:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -1863.7981 16.9946
> 2.4034
>
> EEL -17200.7406 75.1582
> 10.6290
>
> EGB -3249.6527 64.5827
> 9.1334
>
> ESURF 91.3567 1.3775
> 0.1948
>
>
>
> G gas -19064.5387 73.4400
> 10.3860
>
> G solv -3158.2960 64.1112
> 9.0667
>
>
>
> TOTAL -22222.8347 39.9219
> 5.6458
>
>
>
>
>
> Receptor:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -1268.1869 14.0928
> 1.9930
>
> EEL -11557.0789 71.0248
> 10.0444
>
> EGB -2532.0576 57.1271
> 8.0790
>
> ESURF 64.2856 1.1041
> 0.1561
>
>
>
> G gas -12825.2658 66.1471
> 9.3546
>
> G solv -2467.7721 56.9614
> 8.0556
>
>
>
> TOTAL -15293.0379 32.1381
> 4.5450
>
>
>
>
>
> Ligand:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -529.3073 9.3319
> 1.3197
>
> EEL -4684.4887 35.7985
> 5.0627
>
> EGB -1688.9704 26.2775
> 3.7162
>
> ESURF 37.0477 0.6113
> 0.0865
>
>
>
> G gas -5213.7960 37.0299
> 5.2368
>
> G solv -1651.9227 26.1219
> 3.6942
>
>
>
> TOTAL -6865.7187 22.1937
> 3.1387
>
>
>
>
>
> Differences (Complex - Receptor - Ligand):
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -66.3039 4.2329
> 0.5986
>
> EEL -959.1730 34.5550
> 4.8868
>
> EGB 971.3753 32.7146
> 4.6265
>
> ESURF -9.9766 0.3725
> 0.0527
>
>
>
> DELTA G gas -1025.4769 34.3707
> 4.8607
>
> DELTA G solv 961.3987 32.5152
> 4.5983
>
>
>
> DELTA TOTAL -64.0781 6.3096
> 0.8923
>
>
>
>
>
>
> ----------------------------------------------------------------------------
> ---
>
>
> ----------------------------------------------------------------------------
> ---
>
>
>
> POISSON BOLTZMANN:
>
>
>
> Complex:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -1863.7981 16.9946
> 2.4034
>
> EEL -17200.7406 75.1582
> 10.6290
>
> EPB -3190.9098 65.7247
> 9.2949
>
> ENPOLAR 1933.4589 6.8742
> 0.9722
>
> EDISPER -1134.8693 6.9333
> 0.9805
>
>
>
> G gas -19064.5387 73.4400
> 10.3860
>
> G solv -2392.3202 64.9746
> 9.1888
>
>
>
> TOTAL -21456.8589 44.3294
> 6.2691
>
>
>
>
>
> Receptor:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -1268.1869 14.0928
> 1.9930
>
> EEL -11557.0789 71.0248
> 10.0444
>
> EPB -2471.4166 55.7345
> 7.8820
>
> ENPOLAR 1323.4880 5.2717
> 0.7455
>
> EDISPER -791.2302 4.6135
> 0.6525
>
>
>
> G gas -12825.2658 66.1471
> 9.3546
>
> G solv -1939.1588 54.5734
> 7.7178
>
>
>
> TOTAL -14764.4246 36.1469
> 5.1119
>
>
>
>
>
> Ligand:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -529.3073 9.3319
> 1.3197
>
> EEL -4684.4887 35.7985
> 5.0627
>
> EPB -1664.1943 27.4311
> 3.8793
>
> ENPOLAR 660.9497 3.2883
> 0.4650
>
> EDISPER -445.7195 3.9547
> 0.5593
>
>
>
> G gas -5213.7960 37.0299
> 5.2368
>
> G solv -1448.9641 27.7526
> 3.9248
>
>
>
> TOTAL -6662.7601 26.7643
> 3.7850
>
>
>
>
>
> Differences (Complex - Receptor - Ligand):
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> ----------------------------------------------------------------------------
> ---
>
> VDWAALS -66.3039 4.2329
> 0.5986
>
> EEL -959.1730 34.5550
> 4.8868
>
> EPB 944.7011 33.8872
> 4.7924
>
> ENPOLAR -50.9787 1.8037
> 0.2551
>
> EDISPER 102.0803 2.6804
> 0.3791
>
>
>
> DELTA G gas -1025.4769 34.3707
> 4.8607
>
> DELTA G solv 995.8027 33.8122
> 4.7818
>
>
>
> DELTA TOTAL -29.6742 7.9567
> 1.1252
>
>
>
>
>
>
> ----------------------------------------------------------------------------
> ---
>
>
> ----------------------------------------------------------------------------
> ---
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 19 2015 - 08:30:06 PDT
