Dear amber users,
I used following protocol for MD simulation for several ligands against same protein
run_1minimize
restrained energy minimization to minimize water molecules and counterions only
run_2minimize
energy minimization to minimize the entire system
run_3md
heat up system with protein restraints 20ps
run_4md
equilibrate density with protein restraints 1000 ps
run_5md
production run 30ns
I used the production run trajectory, receptor, ligand, complex prmtop files, complex-solvated pmtop files to calculate binding free energy using MM-GBSA and entropy was calculated by Quasi-Harmonic entropy calculation.
However, I am getting positive value for Delta G
Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=3000, verbose=1,netcdf=1,
| entropy=1,
|/
|&gb
| igb=2, qm_theory = 'PM3', saltcon=0.100
|/--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: complex_solvated.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 5md.mdcrd
|
|Receptor mask: ":1-154"
|Ligand mask: ":155"
|Ligand residue name is "UNK"
|
|Calculations performed using 3000 complex frames.
|
|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: 16.4567 16.6171 2402.4677 2435.5417
Receptor: 16.4251 16.5864 2344.5604 2377.5715
Ligand: 13.4823 11.8682 73.5646 98.9151
DELTA S: -13.4507 -11.8374 -15.6573 -40.9449
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1245.6405 17.6262 0.3218
EEL -10872.8419 153.8459 2.8088
EGB -2026.9272 132.6516 2.4219
ESURF 64.0573 1.8536 0.0338
G gas -12118.4825 156.6999 2.8609
G solv -1962.8699 131.3702 2.3985
TOTAL -14081.3524 59.2281 1.0814
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1194.1416 17.5012 0.3195
EEL -10739.8200 153.9997 2.8116
EGB -2018.5959 132.9756 2.4278
ESURF 63.9603 1.8511 0.0338
G gas -11933.9616 156.9558 2.8656
G solv -1954.6356 131.6806 2.4041
TOTAL -13888.5972 59.7499 1.0909
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -7.5750 2.0908 0.0382
EEL -127.2611 2.4619 0.0449
EGB -30.1386 1.1117 0.0203
ESURF 5.3230 0.0487 0.0009
G gas -134.8361 3.3247 0.0607
G solv -24.8156 1.0960 0.0200
TOTAL -159.6517 3.0963 0.0565
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -43.9240 3.6080 0.0659
EEL -5.7609 3.3182 0.0606
EGB 21.8073 3.2526 0.0594
ESURF -5.2260 0.3916 0.0071
DELTA G gas -49.6849 5.2006 0.0949
DELTA G solv 16.5813 3.1147 0.0569
DELTA TOTAL -33.1035 3.4451 0.0629
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Quasi-harmonic Entropy Approximation: DELTA G binding = 7.8414
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using different ligand against protein and follwing same protocol I got WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE.
In addition to VDWAALS, EEL, EGB and ESURF I got values for BOND , ANGLE, DIHED, 1-4 VDW, 1-4 EEL too. The Delta G was positive in this case also.
| Run on Thu Jan 2 07:11:57 2014
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=3000, verbose=1,netcdf=1,
| entropy=1,
|/
|&gb
| igb=2, qm_theory = 'PM3', saltcon=0.100
|/--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: complex_solvated.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 5md.mdcrd
|
|Receptor mask: ":1-154"
|Ligand mask: ":155"
|Ligand residue name is "UNK"
|
|Calculations performed using 3000 complex frames.
|
|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: 16.4531 16.6222 2422.9884 2456.0637
Receptor: 16.4251 16.5858 2373.0474 2406.0583
Ligand: 13.3714 11.4856 63.6693 88.5264
DELTA S: -13.3434 -11.4493 -13.7283 -38.5210
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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 502.3616 18.8777 0.3447
ANGLE 1372.5913 30.2290 0.5519
DIHED 2775.0726 23.1393 0.4225
VDWAALS -1234.5779 22.3262 0.4076
EEL -10728.2002 165.9006 3.0289
1-4 VDW 599.5937 10.5785 0.1931
1-4 EEL 4764.7011 37.4519 0.6838
EGB -2120.6543 164.5357 3.0040
ESURF 64.6350 2.1923 0.0400
G gas -1948.4579 180.1894 3.2898
G solv -2056.0194 163.0035 2.9760
TOTAL -4004.4772 39.7967 0.7266
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 486.3270 18.6276 0.3401
ANGLE 1338.2341 29.7430 0.5430
DIHED 2734.3702 23.0076 0.4201
VDWAALS -1182.3317 21.4647 0.3919
EEL -10612.6402 163.2855 2.9812
1-4 VDW 573.6460 10.4485 0.1908
1-4 EEL 4752.3195 37.9485 0.6928
EGB -2110.2623 164.6202 3.0055
ESURF 65.0172 2.0815 0.0380
G gas -1910.0751 178.6794 3.2622
G solv -2045.2451 163.1962 2.9795
TOTAL -3955.3202 38.4262 0.7016
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 16.0346 3.3559 0.0613
ANGLE 34.3571 4.3665 0.0797
DIHED 40.7029 3.5357 0.0646
VDWAALS -9.0212 1.5387 0.0281
EEL -101.6651 3.0428 0.0556
1-4 VDW 25.9476 1.7246 0.0315
1-4 EEL 12.3816 5.4734 0.0999
EGB -40.6722 3.8112 0.0696
ESURF 4.7384 0.0582 0.0011
G gas 18.7376 6.8351 0.1248
G solv -35.9338 3.7993 0.0694
TOTAL -17.1961 6.1897 0.1130
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0001 0.0000
ANGLE -0.0000 0.0001 0.0000
DIHED -0.0005 0.0079 0.0001
VDWAALS -43.2251 4.3363 0.0792
EEL -13.8948 8.8425 0.1614
1-4 VDW -0.0000 0.0000 0.0000
1-4 EEL -0.0000 0.0001 0.0000
EGB 30.2801 8.1537 0.1489
ESURF -5.1206 0.4126 0.0075
DELTA G gas -57.1204 10.0633 0.1837
DELTA G solv 25.1595 7.9923 0.1459
DELTA TOTAL -31.9609 3.8195 0.0697
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using Quasi-harmonic Entropy Approximation: DELTA G binding = 6.5600
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
What mistake I am making ?
I read in one forum that such error can be due to small production run. Is 30ns not good enough to calculate binding free energy
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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Received on Thu Jan 02 2014 - 03:00:02 PST
