Jianrong,
You can use ptraj to "trajout" a few (3) snapshots into a short tram
file. Check out the Amber basic tutorials on further details.
Ray
On Thu, Nov 29, 2012 at 10:51 PM, Ðì¼ûÈÝ <gjtigergj.163.com> wrote:
> Hi Ray Luo,
>
> Could you tell me the way to extract snapshots from the whole trajectory?
>
> Thx a lot,
>
>
>
>
> Jianrong Xu
>
> ·¢¼þÈË£º Ray Luo
> ·¢ËÍʱ¼ä£º 2012-11-30 11:24
> ÊÕ¼þÈË£º AMBER Mailing List
> Ö÷Ì⣺ 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, Ðì¼ûÈÝ <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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ??? via foxmail
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 30 2012 - 09:30:01 PST
