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 Mon May 28 2012 - 07:00:02 PDT
