Have you applied all of the bug fixes? Do the normal amber tests pass? In
particular, the trajene tests.
All the best,
Jason
On Mon, Jan 3, 2011 at 12:58 PM, Wei Huang <whuang.cct.lsu.edu> wrote:
> 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
> >> _______________________________________________
> >> AMBER mailing list
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> 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 - 16:00:03 PST
