Hi all,
I ran a 10ns MD simulation (all the topology files were made using the same
procedures and the same force field) for a protein-ligand complex, and I
used the MMPBSA.py script to calculate the binding energy. I noted that the
1-4 nonbonded interactions do not completely cancel out in the total
binding free energy, resulting in a large positive value for deltaG.
Can anyone tell me what could be the cause of this error?
Thanks,
Renato
| Run on Mon Oct 19 13:00:46 2015
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
|startframe=401, endframe=2000, interval=2,
|keep_files=2, verbose=1,
|/
|&gb
| igb=2,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: ../01-topology/p53pb1-MS03-com.prmtop
|Complex topology file: ../01-topology/p53pb1-MS03-com_gas.prmtop
|Receptor topology file: ../01-topology/p53pb1_rec.prmtop
|Ligand topology file: ../01-topology/MS03-lig.prmtop
|Initial mdcrd(s): md.nc
|
|Receptor mask: ":1-242"
|Ligand mask: ":243"
|Ligand residue name is "<0>"
|
|Calculations performed using 800 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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 749.9153 22.8509
0.8079
ANGLE 1907.7526 34.1289
1.2066
DIHED 2353.7020 18.9509
0.6700
VDWAALS -1865.8201 22.0098
0.7782
EEL -18333.6598 99.9502
3.5338
1-4 VDW 24170.3751 102.8768
3.6372
1-4 EEL 10561.4546 39.4539
1.3949
EGB -3029.4324 82.7667
2.9262
ESURF 79.4987 1.8955
0.0670
G gas 19543.7197 140.8169
4.9786
G solv -2949.9337 81.7106
2.8889
TOTAL 16593.7860 111.0293
3.9255
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 740.3852 22.7670
0.8049
ANGLE 1880.5317 34.1086
1.2059
DIHED 2333.7538 18.8189
0.6653
VDWAALS -1828.3004 21.6050
0.7639
EEL -18151.7131 104.2307
3.6851
1-4 VDW 868.8332 12.2155
0.4319
1-4 EEL 10547.3401 39.8234
1.4080
EGB -3127.9186 86.3691
3.0536
ESURF 81.0024 1.8407
0.0651
G gas -3609.1695 103.0658
3.6439
G solv -3046.9161 85.3087
3.0161
TOTAL -6656.0856 44.5797
1.5761
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 9.5300 2.6855
0.0949
ANGLE 27.2209 3.5335
0.1249
DIHED 19.9482 2.4322
0.0860
VDWAALS -2.1882 1.6912
0.0598
EEL -15.6794 3.8096
0.1347
1-4 VDW 1434.5710 6.4096
0.2266
1-4 EEL -159.0709 4.3259
0.1529
EGB -70.8238 1.5366
0.0543
ESURF 2.9300 0.0156
0.0006
G gas 1314.3316 7.8732
0.2784
G solv -67.8938 1.5334
0.0542
TOTAL 1246.4378 7.6494
0.2704
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 -0.0000 0.0000
0.0000
VDWAALS -35.3315 2.6688
0.0944
EEL -166.2673 13.0078
0.4599
1-4 VDW 21866.9709 101.5898
3.5917
1-4 EEL 173.1854 0.5204
0.0184
EGB 169.3100 11.1054
0.3926
ESURF -4.4337 0.2677
0.0095
DELTA G gas 21838.5576 102.8667
3.6369
DELTA G solv 164.8763 10.9990
0.3889
DELTA TOTAL 22003.4338 101.6630
3.5943
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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Received on Mon Oct 19 2015 - 14:30:03 PDT
