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Installation

This page describes commonly reported installation problems and possible solutions.

I cannot find the amber.python executable

Solution:

  1. Make sure that you have installed Ambertools20 and sourced the amber.sh(zch) file
  2. If you installed AmberTools20 from conda, use the Python executable from that environment
I get an error related to MPI when I try to install gmx_MMPBSA

If you get an error like this: 

error: Cannot compile MPI programs. Check your configuration!!!

Solution:

Try installing the OpenMPI library:

 sudo apt install openmpi-bin libopenmpi-dev openssh-client

or reinstall it:

sudo apt install --reinstall openmpi-bin libopenmpi-dev openssh-client
I cannot find the gmx_MMPBSA executable

Solution:

  1. Make sure that you have installed gmx_MMPBSA (See here)
  2. Check whether the Miniconda bin folder is in PATH (see here)
  3. Check whether the gmx_MMPBSA executable has execute permission
When I run gmx_MMPBSA I get this error ModuleNotFoundError: No module named 'parmed'

Solution:

See issue 2 for the solution.

Last update: August 29, 2026 16:48:15
Created: April 23, 2021 16:42:12
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