Hello Bill,
I got the same problem . When I use AmberTools1.5(with .bugfix27), the Std. Dev. is very high. Dose AmberTool12 help in this case?
Cao Yang,
Zhejiang University
At 2012-05-28 21:55:41,"Bill Miller III" <brmilleriii.gmail.com> wrote:
>Many changes were made to the MMPBSA.py code between AmberTools 1.5 and
>AmberTools 12, including the way standard deviations were calculated. Let
>us know if the problem is still not fixed in AmberTools 12.
>
>-Bill
>
>On Sat, May 26, 2012 at 11:20 AM, manikanthan bhavaraju
><mhb75.msstate.edu>wrote:
>
>> Dear All,
>>
>> I am presently calculating entropy using MMPBSA of ambertools1.5.
>> The standard deviation of the entropy in the final.dat was very high
>>
>> Complex:
>> Entropy Term Average Std. Dev.
>> -----------------------------------------------------------
>> Translational: 17.5071 0.0000
>> Rotational: 18.4088 0.0067
>> Vibrational: 5787.4771 6.4270
>> Total: 5823.3931 6.4273
>>
>>
>> Receptor:
>> Entropy Term Average Std. Dev.
>> -----------------------------------------------------------
>> Translational: 17.5029 0.0000
>> Rotational: 18.4087 0.0070
>> Vibrational: 5761.3141 8.3323
>> Total: 5797.2257 8.3370
>>
>>
>> Ligand:
>> Entropy Term Average Std. Dev.
>> -----------------------------------------------------------
>> Translational: 12.7742 0.0000
>> Rotational: 10.4609 0.0062
>> Vibrational: 22.5967 0.0242
>> Total: 45.8319 0.0181
>>
>>
>> DELTA S total= -19.6645 +/- 36.9160
>>
>> Below instruction was followed according to one of the previous posting
>>
>> (You should be able to patch AmberTools 1.5 with bugfix.27 (I
>> suggest applying all bugfixes), rebuild MMPBSA.py (cd
>> $AMBERHOME/AmberTools/src/mmpbsa_py && make) and then just run the command
>>
>> MMPBSA [original command-line arguments] -rewrite-output )
>>
>> Still I am getting the same output. Presently I am testing
>> ambertools12 and waiting for the results. Does anyone knows how to
>> fix ambertools1.5?
>> Please let me know about it.
>>
>>
>> thanks,
>> mani
>>
>> --
>>
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>>
>
>
>
>--
>Bill Miller III
>Quantum Theory Project,
>University of Florida
>Ph.D. Graduate Student
>352-392-6715
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Received on Tue May 29 2012 - 00:00:02 PDT
