Re: [AMBER] MMPBSA error

From: Jason Swails <>
Date: Fri, 27 Mar 2015 13:56:03 -0400

> On Mar 27, 2015, at 12:39 PM, Abhishek Tyagi <> wrote:
> Hi,
> this is running on gnu cluster on serial installation, I found that for the first problem when i set igb=1, MMGBSA is running, but when it is set igb=5, it shows the error
> File "/ghome/atyagiaa/amber14/bin/", line 96, in <module>
> app.run_mmpbsa()
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/", line 218, in run_mmpbsa
>, self.stdout)
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/", line 79, in run
>, stdout=stdout, stderr=stderr)
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/", line 148, in run
> self.prmtop))
> CalcError: /ghome/atyagiaa/amber14/bin/sander failed with prmtop complex.prmtop!
> Exiting. All files have been retained.

Look in the Mdout file as Kenneth suggested. It is likely that an error message was printed there. All that you've told us here is that something went wrong.

> for the second problem: I have followed the installation guide as follows:
> ./configure -mpi gnu
> make install
> export DO_PARALLEL='mpirun -np 16’
> make test.parallel
> everything finished fine, but when I had checked AMBERHOME/bin/ their is no file in the folder.
> what could be the reason

Maybe mpi4py did not install correctly. Did you see a message about that in the build log? If the mpi4py build fails, I don't think will be installed.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Mar 27 2015 - 11:00:02 PDT
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