Installation

Note

If you have already installed the code, please uninstall before installing the new version. $ pip uninstall ffparam

Note

If you have downloaded ffparam v1.0 or v1.1, follow the link for Installation instructions for v1.0 or v1.1.

If you have access to https://github.com/mackerell-lab/ , you can clone the package `git clone https://github.com/mackerell-lab/ffparam.git`. Else get the package from http://ffparam.umaryland.edu. Follow these steps to install FFParam.

Use conda for dependency installation

  1. You can install the dependency packages using conda package manager which is a part of the Anaconda Python distribution (available from https://www.anaconda.com/distribution/). Anaconda installation includes python, conda package manager and many other scientific packages. Alternatively, Miniconda can be installed (available from https://docs.conda.io/en/latest/miniconda.html), which includes only python and the conda package manager.

  2. Once Anaconda/Miniconda is installed, you can perform the following actions on your terminal for installing the dependency packages:

  • $ conda create -n ffpenv openmm psi4 -c conda-forge -c psi4

Note

This should create a conda enviornment named ffpenv and installs OpenMM (from channel conda-forge) and Psi4 (from channel psi4) in the same enviornment. OpenMM is required for MM calculations, i.e. if you do not have access to CHARMM, you may alternatively use OpenMM for MM calculation. Psi4 is required for QM calculations, i.e. if you want to run QM jobs on your desktop machine, you may install it. You can also run QM calculation using Gaussian software.

  • $ conda install -n ffpenv -c conda-forge libblas liblapack

Note

libblas and liblapack is required for installing LSFITPAR (You may now perform separate installation of lsfitpar; Obtain the code as $ git clone https://github.com/kennovo/lsfitpar.git ).

  • $ conda activate ffpenv

  1. Untar the package, change to ffparam directory. You should see setup.py file in there. Run the following command:

  • $ tar -xvzf ffparam_v1.2.0.tar.gz

  • $ cd ffparam_v1.2.0

  • $ pip install .

  1. This should install the package and its build dependencies (PyOpenGL,PySide2,matplotlib,RDKit,paramiko,pillow) in ffpenv enviornment. While ffpenv enviornment is active, type `ffparam-gui` on terminal to launch the GUI application.

  • $ ffparam-gui

Enjoy Parametrization!!!

Installation instructions for v1.0 or v1.1

  • $ conda create -n ffpenv openmm psi4 -c conda-forge -c psi4

  • $ conda install -n ffpenv -c conda-forge rdkit freeglut libblas liblapack

  • $ conda install -n ffpenv -c anaconda paramiko pillow

  • $ conda activate ffpenv

  • $ tar -xvzf ffparam_v1.1.0.tar.gz

  • $ cd ffparam_v1.1.0

  • $ python setup.py install

  • $ ffparam-gui