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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 06 2017 - 20:00:03 PDT
