Hi all,
When I use only &pb in my MMPBSA calculations I obtain a reasonable value for EPB, but when I set idecomp=3 the EPB was about 10x smaller in the final_result_mmpbsa file (EPB 67.5297 ). I used the same input files and all other energies are indeed identical. Is that a bug? May I consider that the decomposition energies are correct?
Regards,
Filip
FINAL_RESULTS_MMPBSA error:
Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
|startframe=8001, endframe=10000, interval=25, strip_mask=":WAT,Cl-", verbose=1,
|# entropy=1,
|/
|#&gb
|# igb=2, saltcon=0.100
|#/
|&pb
| istrng=0.100,
|/
|#&decomp
|# idecomp=3, print_res="68-73; 59-67; 74-96; 107-130; 157-167"
|# dec_verbose=1,
|#/
|#&rism
|# polardecomp=1, thermo='gf'--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: 2IOG.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): ProdER.mdcrd
|
|Receptor mask: ":1-96"
|Ligand mask: ":97-181"
|
|Calculations performed using 80 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1300.4345 18.8683 2.1095
EEL -12945.1069 74.5359 8.3334
EPB -1914.8786 63.0355 7.0476
ENPOLAR 1402.5128 8.0609 0.9012
EDISPER -873.7300 9.5301 1.0655
G gas -14245.5414 71.0483 7.9434
G solv -1386.0958 61.4583 6.8712
TOTAL -15631.6372 37.8815 4.2353
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -636.0225 14.8670 1.6622
EEL -6543.5816 59.8964 6.6966
EPB -1447.8124 53.1049 5.9373
ENPOLAR 785.3782 7.4245 0.8301
EDISPER -537.1198 10.6839 1.1945
G gas -7179.6041 60.2133 6.7321
G solv -1199.5540 53.9111 6.0274
TOTAL -8379.1581 30.2407 3.3810
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -561.7187 10.8015 1.2076
EEL -5654.4483 52.6886 5.8908
EPB -1220.6693 35.1604 3.9311
ENPOLAR 699.3572 5.2038 0.5818
EDISPER -481.4802 5.2586 0.5879
G gas -6216.1670 52.5901 5.8797
G solv -1002.7923 33.8162 3.7808
TOTAL -7218.9593 37.4935 4.1919
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -102.6933 5.4243 0.6065
EEL -747.0770 35.9132 4.0152
EPB 753.6030 33.1830 3.7100
ENPOLAR -82.2225 3.7455 0.4188
EDISPER 144.8700 4.5622 0.5101
DELTA G gas -849.7703 36.6566 4.0983
DELTA G solv 816.2504 33.6160 3.7584
DELTA TOTAL -33.5198 10.8837 1.2168
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
nput file for running PB and GB
|&general
|startframe=8001, endframe=10000, interval=25, strip_mask=":WAT,Cl-", verbose=1,
|# entropy=1,
|/
|#&gb
|# igb=2, saltcon=0.100
|#/
|&pb
| istrng=0.100,
|/
|&decomp
| idecomp=3, print_res="68-73; 59-67; 74-96; 107-130; 157-167"
| dec_verbose=1,
|#/
|#&rism
|# polardecomp=1, thermo='gf'--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: 2IOG.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): ProdER.mdcrd
|
|Receptor mask: ":1-96"
|Ligand mask: ":97-181"
|
|Calculations performed using 80 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1300.4345 18.8683 2.1095
EEL -12945.1069 74.5359 8.3334
EPB -53.3041 8.6451 0.9666
ENPOLAR 1402.5128 8.0609 0.9012
EDISPER -873.7300 9.5301 1.0655
G gas -14245.5414 71.0483 7.9434
G solv 475.4787 10.1290 1.1325
TOTAL -13770.0627 70.6477 7.8986
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -636.0225 14.8670 1.6622
EEL -6543.5816 59.8964 6.6966
EPB -40.3898 10.5803 1.1829
ENPOLAR 785.3782 7.4245 0.8301
EDISPER -537.1198 10.6839 1.1945
G gas -7179.6041 60.2133 6.7321
G solv 207.8686 11.9526 1.3363
TOTAL -6971.7355 57.7394 6.4555
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -561.7187 10.8015 1.2076
EEL -5654.4483 52.6886 5.8908
EPB -80.4440 9.0166 1.0081
ENPOLAR 699.3572 5.2038 0.5818
EDISPER -481.4802 5.2586 0.5879
G gas -6216.1670 52.5901 5.8797
G solv 137.4330 8.9145 0.9967
TOTAL -6078.7340 51.8037 5.7918
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -102.6933 5.4243 0.6065
EEL -747.0770 35.9132 4.0152
EPB 67.5297 11.5401 1.2902
ENPOLAR -82.2225 3.7455 0.4188
EDISPER 144.8700 4.5622 0.5101
DELTA G gas -849.7703 36.6566 4.0983
DELTA G solv 130.1771 11.4431 1.2794
DELTA TOTAL -719.5931 37.1032 4.1483
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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Received on Thu Dec 19 2013 - 23:30:02 PST
