Re: [AMBER] app.run_mmpbsa() and mdout files were not created

From: divyabharathi korlepara <>
Date: Thu, 3 Dec 2020 20:32:23 +0530

Hi David,
            It is working with serial version. The parallel version has som
            I ran the test files with serial it got passed.
            The parallel test is giving me the error
  File "/home/*/softwares/amber20_src/bin/", line 97, in
line 857, in check_for_bad_input
    raise InputError('You did not specify any type of calculation!')
InputError: You did not specify any type of calculation!
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
system msg for write_line failure : Bad file descriptor

Dr. Divya Bharathi,
Post Doctoral Fellow,

On Thu, Dec 3, 2020 at 7:24 PM David A Case <> wrote:

> On Thu, Dec 03, 2020, divyabharathi korlepara wrote:
> > I am trying to use program to get binding
> >affinities. I am using amber20tools for this purpose.
> Does everything work OK with itself? That will help narrow
> down the problem. It looks like you are analyzing only a fairly small
> number of frames: do you really need the parallel version.
> Do the test cases work? That will also help see if there is (perhaps)
> some problem related to python2 vs python3.
> [Aside to the list: our python and mmpbsa experts have moved on to
> "real" jobs. It would be great if someone who uses these programs
> regularly would be willing to help out in debugging.]
> ...thanks...dac
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Received on Thu Dec 03 2020 - 07:30:02 PST
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