Hi Ray Luo,
Could you tell me the way to extract snapshots from the whole trajectory?
Thx a lot,
Jianrong Xu
发件人： Ray Luo
发送时间： 2012-11-30 11:24
收件人： AMBER Mailing List
主题： Re: [AMBER] The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model.
My guess is that you implicitly used different sets of radii for PB calculations. But you are welcome to email me the input files and a few snapshots off the list for confirmation
Ray Luo, Ph.D.
On Nov 29, 2012, at 6:43 PM, 徐见容 <gjtigergj.163.com> wrote:
> 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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>
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Received on Thu Nov 29 2012 - 23:00:02 PST
