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Installing gmx_MMPBSA

Requirements

gmx_MMPBSA requires GROMACS (series 4.x.x or 5.x.x or 20xx.x) and AmberTools20 or 21 to be installed in your machine with Python3. gmx_MMPBSA has been tested with GROMACS 4.6.7, 5.1.2, 2018.3, 2020.4 and 2021.3, although it should run smoothly with any GROMACS present in the PATH and that is compatible with the files you are using.

Installing gmx_MMPBSA v1.5.x

Danger

gmx_MMPBSA v1.5.x includes a number of new functionalities and parts of the code have been completely rewritten, hence is incompatible with previous versions.

Currently, gmx_MMPBSA can be installed using two ways:

conda environment
The conda environment provides a clean and efficient way of installing gmx_MMPBSA. It also allows to have different versions of gmx_MMPBSA in isolated environments, thus reducing the possibility of incompatibility with other packages. Installation time is also less since it does not require the compilation of AmberTools or GROMACS. (Recommended, especially if you want to keep older versions of gmx_MMPBSA)
AmberTools compilation
In this way, we assume that you have AmberTools compiled on your machine and that you want to do an installation without worrying about enabling or disabling conda environments. It also involves user compilation of GROMACS, which takes considerable installation time. This way also requires installed packages to be compatible and installation errors are more frequent.

Installation

Installing gmx_MMPBSA using a yml file.

Download env.yml file

// Create a new environment and use the *.yml file to install dependencies
$ conda env create -n gmxMMPBSA --file env.yml

// To use gmx_MMPBSA, just activate the environment
$ conda activate gmxMMPBSA
Copy described intructions
conda env create -n gmxMMPBSA --file env.yml                                    # (1)
conda activate gmxMMPBSA                                                        # (2)
  1. Create the gmxMMPBSA environment and use the *.yml file to install dependencies
  2. Activate gmxMMPBSA environment

Installing dependencies

// Update conda
$ conda update conda

// Create a new environment and activate it
$ conda create -n gmxMMPBSA python=3.9 -y -q 
$ conda activate gmxMMPBSA

// Install mpi4py and AmberTools
$ conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q

// Install updated version of ParmEd
$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

// Install PyQt5 required to use the GUI analyzer tool (gmx_MMPBSA_ana). Not needed for HPC
$ python -m pip install pyqt5

// (Optional) Install GROMACS
$ conda install -c bioconda gromacs==2021.3 -y -q
Copy described intructions
conda update conda
conda create -n gmxMMPBSA python=3.9 -y -q                                      # (1)
conda activate gmxMMPBSA                                                        # (2)
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q      # (3)
python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4 # (4)
python -m pip install pyqt5                                                     # (5)
# Optional
conda install -c bioconda gromacs==2021.3 -y -q                                 # (6)
  1. Create gmxMMPBSA environment
  2. Activate gmxMMPBSA environment
  3. Install dependencies
  4. Install ParmEd
  5. Install PyQt5 if you will use gmx_MMPBSA_ana
  6. (Optional) Install GROMACS if GROMACS is not installed in your machine

INSTALLATION

// INSTALLATION
$ python -m pip install gmx_MMPBSA

UPDATE

// UPDATE
$ python -m pip install gmx_MMPBSA -U

Info

Install/update gmx_MMPBSA from PyPI. PyPI has the latest version of gmx_MMPBSA including stable and beta versions.

INSTALLATION

// INSTALLATION
$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA

UPDATE

// UPDATE
$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

Warning

Install gmx_MMPBSA from the master branch of GitHub repository. This is only recommended for testing new versions or temporary solutions to reported bugs.

Follow the oficial AmberTools installation according to your OS

Note

We asume that AmberTools and their shell environment are correctly configured

INSTALLATION

// Install uodated ParmEd
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
// Install gmx_MMPBSA
$ amber.python -m pip install gmx_MMPBSA                                               

UPDATE

// Update gmx_MMPBSA
$ amber.python -m pip install gmx_MMPBSA -U

Info

Install gmx_MMPBSA from PyPI PyPI has the latest version of gmx_MMPBSA including stable and beta versions.

INSTALLATION

// Install updated ParmEd
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
// Install gmx_MMPBSA
$ amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA     

UPDATE

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

Warning

Install/update gmx_MMPBSA from the master branch of GitHub repository. This version is only recommended to test a new version or to try temporary solutions to reported bugs.

Danger

If you get an error related to installing mpi4py, you may want to install this package manually from conda-forge as follows:

amber.conda install -c conda-forge mpi4py=3.1.3

If you get an error related to pip, you may want to install this package manually as follows:

amber.conda install pip

Miniconda installation

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
---> 100%
$ chmod +x Miniconda3-latest-Linux-x86_64.sh
$ ./Miniconda3-latest-Linux-x86_64.sh
---> 100%
Successful miniconda intallation

Extra Dependencies

gmx_MMPBSA uses some dependencies for other functions independent of calculations or in some cases they may be necessary due to the nature of your OS.

ParmEd

The current version of ParmEd implemented in AmberTools has some limitations that have been resolved in the GitHub repository by its author Jason Swails and others with our help.

Some of these limitations are:

  • Error reading topology when it has insertion codes
  • Error processing topologies generated with the Amber ff19SB force field
  • New PBRadii sets for GAFF and CHARMM force fields

Danger

The gmx_MMPBSA installation process has been optimized to be as straightforward as possible. In rare cases, a few extra dependencies may be needed.

pip

In some cases, the miniconda environment created in the AmberTools compilation does not have the pip module, so any installation that depends on this package will fail. Required only if you did not install gmx_MMPBSA via conda

amber.conda install pip    
Git

Used by gmx_MMPBSA_test to download the GitHub repository to get the examples' folder or to install the development version.

conda install -c anaconda git
or
sudo apt install git 

mpi
In some cases it is necessary to install the MPI dependencies. Required only if you did not install gmx_MMPBSA via conda
sudo apt install openmpi-bin libopenmpi-dev openssh-client
libxcb
If you get an error related to Qt plugins
sudo apt install --reinstall libxcb-xinerama0

Troubleshooting after installation

Once the installation is completed, the following warning may appear:

WARNING: The scripts gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test 
are installed in '/home/user/path_to_amber_install/amber20/miniconda/bin'
which is not on PATH.

This warning is because pip installs the executables (gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test) in installation_path/amber20/miniconda/bin.

You have two options to solve this:

  • Add this folder (*/amber20/miniconda/bin) to PATH:

    export PATH="/path_to_amber_install/amber20/miniconda/bin:$PATH"
    

    Tip

    • This option is more permanent and is recommended if you don't want to activate and deactivate the conda environment
    • Make sure to update path_to_amber_install in the PATH variable
  • Initializing the environment of conda amber:

    amber.conda init bash
    

    You can deactivate like this:

    conda deactivate
    

Note

After using one of the above options, you should be able to run gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test through the terminal

If when running gmx_MMPBSA, you get an error like this:

ModuleNotFoundError: No module named 'parmed'

please see the following issue to see the solution

Autocompletion script

Since gmx_MMPBSA has many flags, we believe that this autocompletion can significantly improve productivity, be more user-friendly and reduce the number of unforced errors. That is why we created this script, which manages the autocompletion of the gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test.

Execution: Enter the following command in the terminal:

source /path/to/ambertools/lib/python3.x/site-packages/GMXMMPBSA/GMXMMPBSA.sh

Tip

If you want it to be activated automatically, add that command to your .bashrc

Warning

  • This script requires that gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test be accessible in PATH
  • If the command-line above end in error, please make sure the file has executed permissions.

    On Ubuntu, Debian, Linux Mint or related:

    • GUI:

      • Right-click on GMXMMPBSA.sh file >

      • Properties >

      • Permissions >

      • Mark the checkbox "Allow to execute the file as a program"

    • Terminal:

      chmod 755 /path/to/ambertools/lib/python3.x/site-packages/GMXMMPBSA/GMXMMPBSA.sh
      

Once you make the source of GMXMMPBSA.sh you can check its operation as follows:

All you have to do is enter the name of the program in the terminal and press the tab key twice:

gmx_MMPBSA <tab> <tab>

Testing the operation of gmx_MMPBSA

After preparing everything to run gmx_MMPBSA, it only remains to check its correct operation. To know how to do it, consult the documentation of gmx_MMPBSA_test


Last update: June 9, 2022 11:58:15
Created: February 8, 2021 07:10:13
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