Re: [AMBER] Problem in using with Amber10

From: Jason Swails <>
Date: Mon, 3 Jan 2011 12:27:18 -0700

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

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,

On Mon, Jan 3, 2011 at 9:52 AM, Wei Huang <> wrote:

> Dear AMBERers,
> I am trying to use the 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:
> "--------------------------------------------------------------------------------
> --------------------------------------------------------------------------------
> 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
> script? I really appreciate your help.
> Thanks,
> Wei
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jan 03 2011 - 11:30:03 PST
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