Dear AMBER community,
Hope you don't mind me bothering you on a Saturday... :)
I would like to ask a few questions regarding MMPBSA.py's implementation in AMBER14. Having read the AMBER14 manual, the MMPBSA.py paper, and a few papers referenced in the manual, I'm a bit confused and unsure about a few things.
What is the default scheme for computing ÄGsolvation in MMPBSA.py in AMBER 14 (default is inp = 2, according to the AMBER14 manual)? I'm specifically talking about the Poisson-Boltzmann computations, i.e. inp=2 in the &pb namelist (which is equivalent to not specifying anything for inp, because 2 is the default value, right)?. I think the manual is a bit unclear. From what I understand
ÄGsolvation = ÄGelectrostatic + ÄGnonpolar
and
ÄGnonpolar = ÄGrepulsive(ÄGcavitation) + ÄGattractive (ÄGdispersion).
Finally:
ÄGrepulsive = ã*SASA + c
where SASA is computed with the LCPO method. Is this correct or is the cavitation term proportional to molecular volume? If so, how is that computed?
Here is a typical output file I get (see below). I see EPB, ENPOLAR, EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is the (repulsive) cavitation term and EDISPER is the (attractive) dispersion term (although in this case ENPOLAR is negative and ECAVITY is positive)?
Also, is the internal PBSA solver in sander linear or nonlinear?
I have seen a lot of recommendations for the "perl" version of MMPBSA, but very little for MMPBSA.py. What settings would you recommend for doing Poisson-Boltzmann calculations on protein - protein complexes?
I would be immensely appreciative if someone can spare a few moments to answer these questions.
Sincerely,
Stefan
| Run on Sat Feb 6 00:47:15 2016
|
|Input file:
|--------------------------------------------------------------
| MM PBSA
|&general
|startframe=1, endframe=1000, interval=1,
|ligand_mask=":151-176", receptor_mask=":1-150",
|verbose=2, netcdf=1,
|/
|&decomp
|idecomp=1,
|/
|&pb
|istrng=0.150, radiopt=0,
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Complex topology file: ras-raf.prmtop
|Receptor topology file: ../7_6/ras.prmtop
|Ligand topology file: ../../4_3/raf.prmtop
|Initial mdcrd(s): centered_traj_2.nc
|Initial Receptor mdcrd(s): ../7_6/ras_centered_2.nc
|Initial Ligand mdcrd(s): ../../4_3/raf_centered_2.nc
|
|Receptor mask: ":1-150"
|Ligand mask: ":151-176"
|
|Calculations performed using 1000 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
-------------------------------------------------------------------------------
BOND 559.1581 19.2297 0.6081
ANGLE 1447.2641 30.1252 0.9526
DIHED 2265.4950 17.8655 0.5650
VDWAALS -1437.0284 19.1765 0.6064
EEL -12640.0035 100.6890 3.1841
1-4 VDW 677.7968 10.8432 0.3429
1-4 EEL 6959.2168 37.4836 1.1853
EPB -2416.0121 82.6641 2.6141
ENPOLAR 1438.3848 8.2909 0.2622
EDISPER -875.0578 11.1865 0.3537
G gas -2168.1009 100.6483 3.1828
G solv -1852.6851 81.8298 2.5877
TOTAL -4020.7860 42.3625 1.3396
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 465.1595 18.3526 0.5804
ANGLE 1226.9118 26.8661 0.8496
DIHED 1936.8447 16.4179 0.5192
VDWAALS -1180.7504 19.0750 0.6032
EEL -10733.1897 102.3469 3.2365
1-4 VDW 575.0592 10.0305 0.3172
1-4 EEL 6791.6278 33.1922 1.0496
EPB -2243.4649 86.4169 2.7327
ENPOLAR 1233.4357 9.0361 0.2857
EDISPER -777.0509 11.0481 0.3494
G gas -918.3370 102.1515 3.2303
G solv -1787.0802 86.5772 2.7378
TOTAL -2705.4172 40.2067 1.2714
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 95.3825 8.6080 0.2722
ANGLE 218.4585 11.5196 0.3643
DIHED 327.9924 7.2065 0.2279
VDWAALS -161.0408 7.4506 0.2356
EEL -1594.8360 40.8275 1.2911
1-4 VDW 101.9945 4.1967 0.1327
1-4 EEL 188.1938 14.5809 0.4611
EPB -518.2112 34.5639 1.0930
ENPOLAR 281.2090 4.0218 0.1272
EDISPER -241.7848 5.1204 0.1619
G gas -823.8551 40.4075 1.2778
G solv -478.7870 34.7465 1.0988
TOTAL -1302.6421 15.4142 0.4874
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND -1.3838 27.9409 0.8836
ANGLE 1.8938 41.9763 1.3274
DIHED 0.6580 25.3112 0.8004
VDWAALS -95.2373 28.0554 0.8872
EEL -311.9778 149.2650 4.7202
1-4 VDW 0.7431 15.3557 0.4856
1-4 EEL -20.6048 52.1473 1.6490
EPB 345.6641 124.4825 3.9365
ENPOLAR -76.2599 12.9060 0.4081
EDISPER 143.7779 16.5354 0.5229
DELTA G gas -425.9088 148.9892 4.7115
DELTA G solv 413.1821 124.0929 3.9242
DELTA TOTAL -12.7267 60.4049 1.9102
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Received on Fri Mar 11 2016 - 23:30:04 PST
