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Installation

Here we describe a series of more frequent reported problems related mainly to the installation process and their possible solutions.

I don't find 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 that python executable
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:

Please try installing/reinstalling the OpenMPI library like this:

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

or this way

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

Solution:

  1. Make sure that you have installed gmx_MMPBSA (See here)
  2. Check if the miniconda bin folder are in the PATH (See here)
  3. Check if the gmx_MMPBSA application has permission to run as a program
When I run gmx_MMPBSA I get this error ModuleNotFoundError: No module named 'parmed'

Solution:

Please see this issue to see the solution

2023-05-27 2023-05-27