Hi Amber users,
I met a problem about the differences between AT1.5 and AT12.
The complex was a protein-protein model, and the binding energy was calculated through MMPBSA.py.
In spite of the same trajectory and the same input parameters, there was significant difference between AT1.5 and AT12 in PBSA solvation model.
The energies were listed below. In GBSA model, the results are almost the same. However, it differs a lot for G solv values and AT12 always show positive binding energy.
Could someone tell me the reason behind it? The item EPB increased by 10% in AT12, why? And what's the difference between ECAVITY in AT1.5 and ENPOLOR & EDISPER in AT12?
Thanks a lot,
AT1.5(GBSA)AT12(GBSA)
ComplexReceptorLigandDifferencesComplexReceptorLigandDifferences
VDWALLS-4229.0344-3897.5431-208.5521-122.9392VDWAALS-4229.0931-3897.6002-208.5508-122.9421
EEL-39082.9365-35397.0309-3016.7502-669.1554EEL-39082.9831-35397.0781-3016.7512-669.1538
EGB-5144.2765-5065.2676-814.8969735.888EGB-5145.5674-5066.4714-815.1027736.0067
ESURF167.0203155.444830.7148-19.1393ESURF167.0153155.446430.7139-19.1449
G gas-43311.9708-39294.5739-3225.3023-792.0946G gas-43312.0762-39294.6783-3225.302-792.0959
G solv-4977.2562-4909.8228-784.1821716.7487G solv-4978.5521-4911.025-784.3888716.8617
TOTAL-48289.227-44204.3968-4009.4844-75.3459TOTAL-48290.6283-44205.7034-4009.6908-75.2342
AT1.5(PBSA)AT12(PBSA)
ComplexReceptorLigandDifferencesComplexReceptorLigandDifferences
VDWAALS-4229.0344-3897.5431-208.5521-122.9392VDWAALS-4229.0931-3897.6002-208.5508-122.9421
EEL-39082.9365-35397.0309-3016.7502-669.1554EEL-39082.9831-35397.0781-3016.7512-669.1538
EPB-5150.5802-5057.9799-818.0918725.4915EPB-4744.186-4731.4803-748.8864736.1807
ECAVITY124.4914115.861522.1635-13.5336ENPOLAR4234.09863922.9437397.8434-86.6885
EDISPER-2145.0458-1999.0636-323.6789177.6966
G gas-43311.9708-39294.5739-3225.3023-792.0946G gas-43312.0762-39294.6783-3225.302-792.0959
G solv-5026.0888-4942.1183-795.9283711.9579G solv-2655.1333-2807.6002-674.7219827.1888
TOTAL-48338.0596-44236.6923-4021.2306-80.1367TOTAL-45967.2095-42102.2786-3900.023835.0929
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Received on Thu Nov 29 2012 - 19:00:03 PST
