Dear Amber-experts,
I am writing to seek help regarding MMPBSA.py calculations on the system that I am studying. Any insight would be really helpful.
I performed all-atomistic MD simulation of a protein complex embedded in lipid bilayer. The protein complex consists of transmembrane domain embedded in the lipid bilayer and large extra-cellular domain in water. The extra-cellular domain is connected to the transmembrane domain with connecting peptide. Now, I am interested in calculating the energy of interaction among the protein domains in water (without the transmembrane domain). To perform this energy calculation using MMPBSA.py I did the following -
1. Extracted a trajectory containing only the only the protein domain in water using the following cpptraj commands -
parm protein+lipid_bilayer.prmtop
trajin Complex_Run1.mdcrd 1500 2500
strip !:1-201,255-497,553-639,680-751,792-878,919-1001
trajout ectodomain.nc nc
go
quit
2. Generated prmtop files considering one part of the protein domain in water as 'receptor' and the other part as 'ligand'. Used the following single script to generate the prmtop files -
source /cluster/apps/amber16/gnu/patch_20160109/amber16/dat/leap/cmd/oldff/leaprc.ff99SBildn
receptor = loadpdb rec.pdb
ligand = loadpdb lig.pdb
complex = combine {receptor ligand}
set default PBRadii mbondi2
bond receptor.22.SG receptor.86.SG
bond receptor.133.SG receptor.183.SG
bond receptor.158.SG receptor.372.SG
bond receptor.224.SG receptor.276.SG
bond receptor.346.SG receptor.411.SG
bond receptor.462.SG receptor.511.SG
bond receptor.548.SG receptor.584.SG
saveAmberParm receptor rec.prmtop rec.inpcrd
bond ligand.18.SG ligand.67.SG
bond ligand.113.SG ligand.154.SG
saveAmberParm ligand lig.prmtop lig.inpcrd
saveAmberParm complex complex.prmtop complex.inpcrd
quit
3. tleap command with the script in step 2 adds an OXT atom to complete the valency on the residue upto which the protein domain in water was considered for this calculation. Since this is not in harmony with the extracted trajectory (step 1 above) from explicit water-membrane simulation, the OXT atom was removed from each of the prmtop files used parmed command.
parm rec.prmtop
strip .OTX
outparm rec_noOXT.prmtop
quit
parm lig.prmtop
strip .OTX
outparm lig_noOXT.prmtop
quit
parm complex.prmtop
strip .OXT
outparm complex_noOXT.prmtop
quit
4. Finally the MMPBSA.py calculations were performed using the prmtop files generated in step 3.
MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp complex_noOXT.prmtop -rp rec_noOXT.prmtop -lp lig_noOXT.prmtop -y ectodomain.nc -eo Energy-terms.csv
Contents of mmpbsa.in file are as follows -
Input file for running PB and GB
&general
startframe=0,endframe=1000, keep_files=2,verbose=1,interval=2,
/
&gb
igb=5, saltcon=0.100
/
&pb
istrng=0.150, fillratio=4.0, radiopt=0,
The calculation runs fine. But the output Delta Total is large positive value. Any insights in mistakes made in the steps carried out above will be helpful. Also, suggestions regarding finding the energy of interaction among the protein domains will be appreciated. The output in the FINAL_RESULTS_MMPBSA.dat file are as follows -
| Run on Mon Nov 13 14:53:51 2017
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| startframe=0,endframe=1001, keep_files=0,verbose=1,interval=2,
|/
|&gb
| igb=5, saltcon=0.100
|/
|&pb
| istrng=0.150, fillratio=4.0, radiopt=0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Complex topology file: ../complex_noOXT.prmtop
|Receptor topology file: ../rec_noOXT.prmtop
|Ligand topology file: ../lig_noOXT.prmtop
|Initial mdcrd(s): ../../ectodomain.nc
|
|Receptor mask: ":1-603"
|Ligand mask: ":604-773"
|
|Calculations performed using 501 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:
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 2875.0371 49.3551 2.2072
ANGLE 6481.5215 61.1678 2.7355
DIHED 8553.5351 38.6457 1.7283
VDWAALS -105.3838 577.5441 25.8286
EEL -53446.9320 175.0670 7.8292
1-4 VDW 2705.7416 20.3478 0.9100
1-4 EEL 31424.7071 78.9230 3.5295
EGB -10527.5682 149.4302 6.6827
ESURF 259.7666 3.3206 0.1485
G gas -1511.7733 598.3420 26.7587
G solv -10267.8016 147.8432 6.6118
TOTAL -11779.5749 580.5043 25.9609
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 2243.8763 43.0646 1.9259
ANGLE 5040.0612 54.2342 2.4254
DIHED 6698.1385 34.8696 1.5594
VDWAALS -4584.3327 34.4602 1.5411
EEL -41125.1732 154.0434 6.8890
1-4 VDW 2110.8027 18.2972 0.8183
1-4 EEL 23392.1743 74.4550 3.3297
EGB -8002.7933 127.9705 5.7230
ESURF 213.6169 3.1438 0.1406
G gas -6224.4529 161.8473 7.2380
G solv -7789.1764 126.3621 5.6511
TOTAL -14013.6293 77.9233 3.4848
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 633.2935 23.0719 1.0318
ANGLE 1445.6526 30.2798 1.3542
DIHED 1870.8840 17.1543 0.7672
VDWAALS -1270.7269 18.7134 0.8369
EEL -12140.8710 109.4239 4.8936
1-4 VDW 594.2000 10.9983 0.4919
1-4 EEL 8008.0915 39.3401 1.7593
EGB -2771.2094 92.0633 4.1172
ESURF 62.6303 1.8993 0.0849
G gas -859.4765 109.5406 4.8988
G solv -2708.5791 90.9516 4.0675
TOTAL -3568.0556 43.8003 1.9588
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -2.1327 1.1456 0.0512
ANGLE -4.1922 1.5992 0.0715
DIHED -15.4874 1.5998 0.0715
VDWAALS 5749.6758 576.1688 25.7671
EEL -180.8878 49.8494 2.2293
1-4 VDW 0.7390 0.3852 0.0172
1-4 EEL 24.4414 0.2127 0.0095
EGB 246.4345 49.2697 2.2034
ESURF -16.4806 1.0192 0.0456
DELTA G gas 5572.1561 578.1818 25.8571
DELTA G solv 229.9539 48.7950 2.1822
DELTA TOTAL 5802.1100 576.2924 25.7726
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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 2875.0371 49.3551 2.2072
ANGLE 6481.5215 61.1678 2.7355
DIHED 8553.5351 38.6457 1.7283
VDWAALS -105.3838 577.5441 25.8286
EEL -53446.9320 175.0670 7.8292
1-4 VDW 2705.7416 20.3478 0.9100
1-4 EEL 31424.7071 78.9230 3.5295
EPB -10646.4858 151.0742 6.7562
ENPOLAR 6019.7632 16.6587 0.7450
EDISPER -3565.8584 22.3217 0.9983
G gas -1511.7733 598.3420 26.7587
G solv -8192.5811 154.2243 6.8971
TOTAL -9704.3544 580.6887 25.9692
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 2243.8763 43.0646 1.9259
ANGLE 5040.0612 54.2342 2.4254
DIHED 6698.1385 34.8696 1.5594
VDWAALS -4584.3327 34.4602 1.5411
EEL -41125.1732 154.0434 6.8890
1-4 VDW 2110.8027 18.2972 0.8183
1-4 EEL 23392.1743 74.4550 3.3297
EPB -8074.2883 130.2314 5.8241
ENPOLAR 4725.6212 16.3530 0.7313
EDISPER -2859.4343 20.9745 0.9380
G gas -6224.4529 161.8473 7.2380
G solv -6208.1013 132.8090 5.9394
TOTAL -12432.5542 81.8473 3.6603
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 633.2935 23.0719 1.0318
ANGLE 1445.6526 30.2798 1.3542
DIHED 1870.8840 17.1543 0.7672
VDWAALS -1270.7269 18.7134 0.8369
EEL -12140.8710 109.4239 4.8936
1-4 VDW 594.2000 10.9983 0.4919
1-4 EEL 8008.0915 39.3401 1.7593
EPB -2790.9820 93.1083 4.1639
ENPOLAR 1378.4868 9.6170 0.4301
EDISPER -883.6631 12.3160 0.5508
G gas -859.4765 109.5406 4.8988
G solv -2296.1583 94.3783 4.2207
TOTAL -3155.6349 45.4217 2.0313
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -2.1327 1.1456 0.0512
ANGLE -4.1922 1.5992 0.0715
DIHED -15.4874 1.5998 0.0715
VDWAALS 5749.6758 576.1688 25.7671
EEL -180.8878 49.8494 2.2293
1-4 VDW 0.7390 0.3852 0.0172
1-4 EEL 24.4414 0.2127 0.0095
EPB 218.7845 49.2774 2.2038
ENPOLAR -84.3448 5.1132 0.2287
EDISPER 177.2390 8.1231 0.3633
DELTA G gas 5572.1561 578.1818 25.8571
DELTA G solv 311.6786 50.3720 2.2527
DELTA TOTAL 5883.8347 575.1096 25.7197
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Thanking you,
Prithvi Raj Pandey
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Received on Thu Nov 16 2017 - 01:30:02 PST
