Thank you Jason,
finally works!
giulia
2017-07-06 19:58 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
> The van der Waals energies are highly concerning -- there is probably a
> mismatch in trajectory and topology files -- I would recommend visualizing
> them to be sure.
>
> Another thing to try is to set "netcdf=1" in the &general section -- this
> will likely highlight inconsistencies between the topology and coordinate
> files faster with a more helpful error message.
>
> HTH,
> Jason
>
> On Thu, Jul 6, 2017 at 2:45 PM, giulia palermo <giulia.palermo83.gmail.com
> >
> wrote:
>
> > Dear all,
> >
> > I am using MMPBSA for computing the binding energy in a system composed
> by
> > an RNA dimer. In particular, I want to compute the binding energy between
> > the two RNA monomers and compare the results with sistems that include
> > mutations of the RNA bases.
> > While some systems give good results with energies of the order of 200
> > kcal/mol, in some others I get very big and unrealistic energies (>
> 2000000
> > kcal/mol) that worry me a lot.
> >
> > I have checked the topology files and nothing is wrong. I report below
> > Input and output files, such that we could try to understand better what
> is
> > going on. I can also provide a zip file with the data, in case you need
> it
> > for understanding better.
> >
> >
> > Thank you very much
> > Giulia
> >
> >
> >
> > *--- INPUT *
> > &general
> > endframe=2000, keep_files=2, interval=10,
> > entropy=1,
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100, inp=1, radiopt=0,
> > /
> >
> >
> > *---- COMMAND LINE*
> > MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp tutto.top -rp
> > azzurro.top -lp rosa.top -y ../tutto.dcd
> >
> >
> > *----- FINAL RESULTS*
> > | Run on Thu Jun 29 12:49:18 2017
> > |
> > |Input file:
> > |--------------------------------------------------------------
> > |#Input file for running PB and GB in serial
> > |#In the trajectory there are 499 frames.
> > |#Therefore, I tthink that startframe and interval are not needed
> > |&general
> > | endframe=2000, keep_files=2, interval=10,
> > | entropy=1,
> > |/
> > |&gb
> > | igb=2, saltcon=0.100,
> > |/
> > |&pb
> > | istrng=0.100, inp=1, radiopt=0,
> > |/
> > |--------------------------------------------------------------
> > |MMPBSA.py Version=14.0
> > |Complex topology file: tutto.top
> > |Receptor topology file: azzurro.top
> > |Ligand topology file: rosa.top
> > |Initial mdcrd(s): ../tutto.dcd
> > |
> > |Receptor mask: ":1-67"
> > |Ligand mask: ":68-100"
> > |
> > |Calculations performed using 200 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.
> > |All entropy results have units kcal/mol (Temperature is 298.15 K).
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> > ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
> > Translational Rotational Vibrational Total
> > Complex: 16.9612 17.7065 494.4874 529.1551
> > Receptor: 16.6055 17.2566 445.9591 479.8211
> > Ligand: 15.9767 16.0411 378.3947 410.4121
> >
> > DELTA S: -15.6210 -15.5912 -329.8663 -361.0781
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> >
> > GENERALIZED BORN:
> >
> > WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
> > TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 863.5584 52.5209
> > 3.7138
> > ANGLE 1717.9641 128.1270
> > 9.0599
> > DIHED 2440.4157 21.2860
> > 1.5051
> > VDWAALS 2135120.4971 30148132.7015
> > 2131794.9073
> > EEL 61226.6951 1068.2498
> > 75.5367
> > 1-4 VDW 926.7021 120.0454
> > 8.4885
> > 1-4 EEL -9754.6497 62.3446
> > 4.4084
> > EGB -74998.2264 1040.3425
> > 73.5633
> > ESURF 113.6611 1.9806
> > 0.1400
> >
> > G gas 2192541.1829 30148330.3145
> > 2131808.8807
> > G solv -74884.5653 1041.7523
> > 73.6630
> >
> > TOTAL 2117656.6176 30148389.7875
> > 2131813.0861
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 577.6872 36.7050
> > 2.5954
> > ANGLE 1151.5710 79.0534
> > 5.5899
> > DIHED 1624.5403 17.4328
> > 1.2327
> > VDWAALS -1279.7928 99.0867
> > 7.0065
> > EEL 28413.4632 496.7589
> > 35.1262
> > 1-4 VDW 621.0646 61.4803
> > 4.3473
> > 1-4 EEL -6534.2221 45.0564
> > 3.1860
> > EGB -37808.6029 479.2571
> > 33.8886
> > ESURF 83.4961 0.9568
> > 0.0677
> >
> > G gas 24574.3116 564.6386
> > 39.9260
> > G solv -37725.1067 479.7390
> > 33.9227
> >
> > TOTAL -13150.7952 244.3944
> > 17.2813
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 285.8712 20.8172
> > 1.4720
> > ANGLE 566.3930 52.9689
> > 3.7455
> > DIHED 815.8762 12.0968
> > 0.8554
> > VDWAALS -572.5263 461.9426
> > 32.6643
> > EEL 7844.5275 155.4300
> > 10.9906
> > 1-4 VDW 305.6375 59.3613
> > 4.1975
> > 1-4 EEL -3220.4276 28.0315
> > 1.9821
> > EGB -12444.3007 136.4186
> > 9.6462
> > ESURF 41.4453 0.7792
> > 0.0551
> >
> > G gas 6025.3516 567.6487
> > 40.1388
> > G solv -12402.8554 136.9028
> > 9.6805
> >
> > TOTAL -6377.5038 570.3578
> > 40.3304
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND -0.0000 0.0000
> > 0.0000
> > ANGLE 0.0000 0.0000
> > 0.0000
> > DIHED -0.0008 0.0108
> > 0.0008
> > VDWAALS 2136972.8161 30147573.4683
> > 2131755.3636
> > EEL 24968.7044 784.7003
> > 55.4867
> > 1-4 VDW -0.0000 0.0000
> > 0.0000
> > 1-4 EEL -0.0000 0.0001
> > 0.0000
> > EGB -24745.3228 760.5724
> > 53.7806
> > ESURF -11.2804 1.4876
> > 0.1052
> >
> > DELTA G gas 2161941.5197 30147501.4071
> > 2131750.2681
> > DELTA G solv -24756.6032 761.8569
> > 53.8714
> >
> > DELTA TOTAL 2137184.9165 30147578.6055
> > 2131755.7268
> >
> >
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> > Using Quasi-harmonic Entropy Approximation: DELTA G binding =
> 2137545.9947
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> >
> > POISSON BOLTZMANN:
> >
> > WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
> > TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 863.5584 52.5209
> > 3.7138
> > ANGLE 1717.9641 128.1270
> > 9.0599
> > DIHED 2440.4157 21.2860
> > 1.5051
> > VDWAALS 2135120.4971 30148132.7014
> > 2131794.9073
> > EEL 61226.6951 1068.2498
> > 75.5367
> > 1-4 VDW 926.7021 120.0454
> > 8.4885
> > 1-4 EEL -9754.6497 62.3446
> > 4.4084
> > EPB -75058.3000 1034.0505
> > 73.1184
> > ENPOLAR 82.9290 1.7472
> > 0.1235
> >
> > G gas 2192541.1829 30148330.3145
> > 2131808.8807
> > G solv -74975.3710 1035.3117
> > 73.2076
> >
> > TOTAL 2117565.8118 30148379.9697
> > 2131812.3918
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 577.6872 36.7050
> > 2.5954
> > ANGLE 1151.5710 79.0534
> > 5.5899
> > DIHED 1624.5403 17.4328
> > 1.2327
> > VDWAALS -1279.7928 99.0867
> > 7.0065
> > EEL 28413.4632 496.7589
> > 35.1262
> > 1-4 VDW 621.0646 61.4803
> > 4.3473
> > 1-4 EEL -6534.2221 45.0564
> > 3.1860
> > EPB -37965.0848 477.2809
> > 33.7489
> > ENPOLAR 61.2719 0.8830
> > 0.0624
> >
> > G gas 24574.3116 564.6386
> > 39.9260
> > G solv -37903.8129 477.6974
> > 33.7783
> >
> > TOTAL -13329.5014 237.7628
> > 16.8124
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND 285.8712 20.8172
> > 1.4720
> > ANGLE 566.3930 52.9689
> > 3.7455
> > DIHED 815.8762 12.0968
> > 0.8554
> > VDWAALS -572.5263 461.9426
> > 32.6643
> > EEL 7844.5275 155.4300
> > 10.9906
> > 1-4 VDW 305.6375 59.3613
> > 4.1975
> > 1-4 EEL -3220.4276 28.0315
> > 1.9821
> > EPB -12578.2882 135.8807
> > 9.6082
> > ENPOLAR 31.4949 0.5621
> > 0.0397
> >
> > G gas 6025.3516 567.6487
> > 40.1388
> > G solv -12546.7933 136.1909
> > 9.6301
> >
> > TOTAL -6521.4417 568.3437
> > 40.1880
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> > -------------------
> > BOND -0.0000 0.0000
> > 0.0000
> > ANGLE 0.0000 0.0000
> > 0.0000
> > DIHED -0.0008 0.0108
> > 0.0008
> > VDWAALS 2136972.8161 30147573.4682
> > 2131755.3636
> > EEL 24968.7044 784.7003
> > 55.4867
> > 1-4 VDW -0.0000 0.0000
> > 0.0000
> > 1-4 EEL -0.0000 0.0001
> > 0.0000
> > EPB -24514.9270 752.0293
> > 53.1765
> > ENPOLAR -9.8378 1.2653
> > 0.0895
> > EDISPER 0.0000 0.0000
> > 0.0000
> >
> > DELTA G gas 2161941.5197 30147501.4070
> > 2131750.2681
> > DELTA G solv -24524.7648 753.1636
> > 53.2567
> >
> > DELTA TOTAL 2137416.7549 30147577.5534
> > 2131755.6524
> >
> >
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> > Using Quasi-harmonic Entropy Approximation: DELTA G binding =
> 2137777.8330
> > ------------------------------------------------------------
> > -------------------
> > ------------------------------------------------------------
> > -------------------
> > ~
> >
> >
> >
> >
> >
> >
> >
> > ~
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> _______________________________________________
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>
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Received on Sat Jul 08 2017 - 10:30:02 PDT
