Dear all:
I'm planning to use the MMPBSA.py with my protein-protein complex but
before, I wanted to verify my installation by reproducing the results from
the MMPBSA tutorial. I downloaded all the necessary files to perform the
calculation from the tutorial web page (ras-raf_top_mdcrd.tgz).
To do the calculation I used the same command line as the tutorial with the
only difference that I used 8 cpu's (nohup mpirun -np 8
$AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa_1b.in -o FINAL_RESULTS_MMPBSA.dat
-sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
raf.prmtop -y *.mdcrd > progress.log 2>&1 &). There is some difference in
the GENERALIZED BORN part of the calculation but the final results are
similar (my results:DELTA TOTAL -64.0781(AVE) 6.3096(STDD)
0.8923(STDErr);tutorial: DELTA G binding -64.9352(AVE) 6.2195(STDD)
0.8796(STDErr)) but there is a huge difference with the POISSON BOLTZMANN
part (my results:DELTA TOTAL -29.6742(AVE) 7.9567(STDD)
1.1252(STDErr);tutorial: DELTA G binding -86.3878(AVE) 8.1828(STDD)
1.1572(STDErr)).
What could cause the huge difference? I dont think that is my installation
because all the test related to mmpbsa pass without errors. Any comments or
help will be appreciated.
My system:
AMD FX(tm)-8150 Eight-Core Processor
16GB RAM
2 GTX690
Motherboard: GA-990FXA-UD5
Amber 12 (all patches applied)
AmberTools 12 upgraded to 13 (all patches applied)
mpich2
intel compilers version 13.1.1
Bellow is the FINAL_RESULTS_MMPBSA.dat from my calculation. The values from
the tutorial could be found at
http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/FINAL_RESULTS_MMPBSA_parallel.dat
Best Regards,
Anthony Cruz
The results are the fallowing:
| Run on Fri Nov 8 09:55:25 2013
|
|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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Received on Fri Nov 08 2013 - 08:30:02 PST
