Hi Jason,
Yes, you are right. The test for 01_Generalized_Born is not really passed. And also 07_Comprehensive, which is due to the GB part.
It seems that the calculations for GB stop at the minimization steps.
"--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1"
How can I figure out what the problem is? Thanks!
Best,
Wei
On Jan 3, 2011, at 1:27 PM, Jason Swails wrote:
> Hello Wei,
>
> imin = 5 was introduced in amber9, so it should work just fine with
> amber10. If you look at the amber10 manual on page 23, it clearly describes
> the imin = 5 functionality. The imin = 5 trajectory analysis is not
> supported in pmemd, but that is not used in MMPBSA.py.
>
> There is also a problem with the differ script in the test suite in which
> absolute/relative error comparisons will register "PASSED" in some cases
> where it should report "FAILURE", with some cryptic message about
> "ddtmp.FINAL_RESULTS_MMPBSA.dat is short" or something. This has been fixed
> in the new release, but can still be misleading.
>
> Are you trying with GB or PB? Do the tests really pass or not? If the
> tests really pass, then try using the input files provided in the test suite
> for your system and see if that works.
>
> Hope this helps,
> Jason
>
> On Mon, Jan 3, 2011 at 9:52 AM, Wei Huang <whuang.cct.lsu.edu> wrote:
>
>> Dear AMBERers,
>>
>> I am trying to use the MMPBSA.py script to do MM-PBSA calculation for my
>> systems. The amber package I have is amber 10.
>>
>> Although the test runs are all passed, I notice that all the *.mdout file
>> are not completed. They all stuck at the following part:
>>
>> "--------------------------------------------------------------------------------
>> 4. RESULTS
>>
>> --------------------------------------------------------------------------------
>>
>> POST-PROCESSING OF TRAJECTORY ENERGIES
>> trajectory generated by ptraj
>> minimizing coord set # 1"
>>
>> I found that imin=5 is used in the GB/PB calculation. But then I also found
>> the following in the amber10 manual:
>> "imin=5 In &cntrl. Trajectory analysis is not supported."
>>
>> Can I use imin=1 instead of imin=5 here? If yes, how can I change it in the
>> MMPBSA.py script? I really appreciate your help.
>>
>> Thanks,
>> Wei
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Mon Jan 03 2011 - 12:00:05 PST
