-----Original Message-----
From: "ammar mohseni" <a.mohseni.modares.ac.ir>
To: <amber.ambermd.org'>
Date: Wed, 11 Feb 2015 04:25:23 +0330
Subject: MMPBSA
Hi Dear
I have the problem in the result of MMPBSA.
I rerun the tutorial of MMPBSA in amber website.
But my result in FINAL_RESULTS_MMPBSA.dat are different with on the
website.
One of different is the ECAVITY value. This value is not exist in my
result files.
Please help me.
thanks
My result file:
.
| Run on Tue Feb 10 17:10:04 2015
|
|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,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=13.0
|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.
-------------------------------------------------------------------------
-
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-------------------------------------------------------------------------
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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
-------------------------------------------------------------------------
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-------------------------------------------------------------------------
-
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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 -3314.8738 66.2632
9.3710
ENPOLAR 1965.5188 6.3800
0.9023
EDISPER -1157.9116 7.2439
1.0244
G gas -18952.0295 81.3542
11.5052
G solv -2507.2665 65.1908
9.2194
TOTAL -21459.2961 40.2725
5.6954
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 -3340.9508 66.5434
9.4107
ENPOLAR 1956.8205 6.3089
0.8922
EDISPER -1183.2700 6.7784
0.9586
G gas -18850.2679 80.7202
11.4156
G solv -2567.4004 65.4154
9.2511
TOTAL -21417.6682 38.9112
5.5029
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 -30.7649 0.6756
0.0955
ENPOLAR 52.1180 0.2043
0.0289
EDISPER -52.8554 0.3423
0.0484
G gas -7.4395 3.0299
0.4285
G solv -31.5024 0.7468
0.1056
TOTAL -38.9418 3.0656
0.4335
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 56.8420 2.9272
0.4140
ENPOLAR -43.4196 1.2202
0.1726
EDISPER 78.2138 1.4501
0.2051
DELTA G gas -94.3222 3.3476
0.4734
DELTA G solv 91.6362 3.4609
0.4894
DELTA TOTAL -2.6860 3.8116
0.5390
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Received on Wed Feb 11 2015 - 01:30:03 PST
