Hi, all,
I am going through Amber tutorial A3 "MM-PBSA" to learn how to calculate binding energy.
(Webpage: http://ambermd.org/tutorials/advanced/tutorial3/ )
And I find the final PBSA results are quite different from that in the tutorial.
For example, for the receptor-ligand of Estrogen-Raloxifene, my PBSA calculation results are quite different from that on webpage:
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
In brief, my PBSA binding energy is -6.6901, while the results on the webpage is -41.7256 .
My "FINAL_RESULTS_MMPBSA.dat" is the following:
$ cat FINAL_RESULTS_MMPBSA.dat
| Run on Fri May 20 17:42:45 2016
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
| inp=2,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: 1err.solvated.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 1err_prod.mdcrd
|
|Receptor mask: ":1-240"
|Ligand mask: ":241"
|Ligand residue name is "RAL"
|
|Calculations performed using 50 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:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108 2.8441
EEL -16938.6434 84.8707 12.0025
EGB -3506.9860 67.1003 9.4894
ESURF 97.4744 1.3170 0.1863
G gas -18952.0295 81.3542 11.5052
G solv -3409.5116 66.5951 9.4180
TOTAL -22361.5411 36.3100 5.1350
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529 2.6945
EEL -16895.0333 84.6812 11.9757
EGB -3528.7058 67.6664 9.5695
ESURF 101.2621 1.2926 0.1828
G gas -18850.2679 80.7202 11.4156
G solv -3427.4437 67.2065 9.5044
TOTAL -22277.7116 34.9512 4.9428
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320 0.2874
EEL -5.5800 2.0133 0.2847
EGB -28.4852 0.5979 0.0846
ESURF 4.4805 0.0425 0.0060
G gas -7.4395 3.0299 0.4285
G solv -24.0047 0.6040 0.0854
TOTAL -31.4442 3.2513 0.4598
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EGB 50.2050 2.5622 0.3624
ESURF -8.2682 0.2700 0.0382
DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 41.9369 2.4569 0.3475
DELTA TOTAL -52.3853 2.4400 0.3451
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108 2.8441
EEL -16938.6434 84.8707 12.0025
EPB -3243.8422 65.3230 9.2381
ENPOLAR 1965.5188 6.3800 0.9023
EDISPER -1107.5209 6.8746 0.9722
G gas -18952.0295 81.3542 11.5052
G solv -2385.8443 64.1413 9.0709
TOTAL -21337.8739 41.6822 5.8948
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529 2.6945
EEL -16895.0333 84.6812 11.9757
EPB -3269.8301 65.8433 9.3116
ENPOLAR 1956.8205 6.3089 0.8922
EDISPER -1131.1692 6.4443 0.9114
G gas -18850.2679 80.7202 11.4156
G solv -2444.1788 64.7272 9.1538
TOTAL -21294.4467 40.4322 5.7180
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320 0.2874
EEL -5.5800 2.0133 0.2847
EPB -30.7641 0.6756 0.0955
ENPOLAR 52.1180 0.2043 0.0289
EDISPER -50.6514 0.3305 0.0467
G gas -7.4395 3.0299 0.4285
G solv -29.2976 0.7438 0.1052
TOTAL -36.7370 3.0716 0.4344
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EPB 56.7520 3.5086 0.4962
ENPOLAR -43.4196 1.2202 0.1726
EDISPER 74.2997 1.3514 0.1911
DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 87.6321 3.8310 0.5418
DELTA TOTAL -6.6901 3.8563 0.5454
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Could anyone help me?
------------------
LI AnBang
Physics Department, Central China Normal University, China
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Received on Fri May 20 2016 - 20:00:03 PDT
