Hello Amber users,
I have attempted the MMPBSA.py tutorial and got significantly higher delta G binding energies in the Poisson Boltzmann calculation (Please see below).
I have downloaded and run the scripts in the tutorials, Ras-raf (Section 3.1) and Estrogen Receptor and Raloxifene (Section 3.2)
I am using MMPBSA.py (Version=14.0) with ambertools 20
Some differences I have noticed between new and old MMPBSA.py:
1. new uses the mmpbsa_py_energy, old one used sander, (after trying it with Sander, it made no difference).
2. new calculates “ENPOLAR” and “EDISPER” instead of “ECAVITY” and these terms account for the greatest difference between the two calculations.
3. I have noticed that some settings are different, notably, that “ipb” and “inp” are set to 2 in new and 1 in old.
For the Estrogen exercise, I tested it with “ipb” and “inp” set to 1 (there were some warning associated with inp=1) and got a result that is similar to the tutorial (see below). In this calculation EDISPER = 0 while ENPOLAR ~ ECAVITY in the old calculation.
I would like some information on why there is such a big difference in energies and if its ok to calculate binding free energy using MMPBSA.py (Version=14.0) with the settings in the tutorial file (
https://ambermd.org/tutorials/advanced/tutorial3/py_script/files/mmpbsa_2b.in)
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
Ras-raf exercise:
VDWAALS -66.2966 4.2751 0.6046
EEL -959.1803 34.9190 4.9383
EPB 946.4251 34.5128 4.8808
ECAVITY -7.3062 0.3004 0.0425
DELTA G gas -1025.4769 1237.6138 175.0250
DELTA G solv 939.1189 34.5141 4.8810
DELTA G binding = -86.3579 +/- 8.3264 1.1775
_____________________________________________________________________________
Ras-raf, my attempt:
VDWAALS -66.3039 4.2329 0.5986
EEL -959.1730 34.5550 4.8868
EPB 947.1114 33.4524 4.7309
ENPOLAR -50.9787 1.8037 0.2551
EDISPER 101.1385 2.6639 0.3767
DELTA G gas -1025.4769 34.3707 4.8607
DELTA G solv 997.2711 33.4305 4.7278
DELTA TOTAL -28.2058 8.1968 1.1592
_____________________________________________________________________________
Estrogen Receptor and Raloxifene, exercise:
VDWAALS -56.2934 2.9265 0.4139
EEL -38.0300 3.2114 0.4542
EPB 57.6402 3.0642 0.4333
ECAVITY -5.0423 0.1683 0.0238
DELTA G gas -94.3234 18.8778 2.6697
DELTA G solv 52.5978 3.0688 0.4340
DELTA G binding = -41.7256 +/- 2.9618 0.4189
_____________________________________________________________________________
Estrogen Receptor and Raloxifene, my attempt:
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
_____________________________________________________________________________
Estrogen Receptor and Raloxifene, my attempt with ipb=1, inp=1:
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EPB 56.8405 2.9271 0.4140
ENPOLAR -5.5814 0.1540 0.0218
EDISPER 0.0000 0.0000 0.0000
DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 51.2591 2.9325 0.4147
DELTA TOTAL -43.0631 2.8642 0.4051
Kind regards,
Ali Kusay
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
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Received on Wed Mar 24 2021 - 07:00:03 PDT
