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
------------------------------------------------------------
-------------------
------------------------------------------------------------
-------------------
~
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Received on Thu Jul 06 2017 - 12:00:03 PDT
