Date: June 20-24, 2022

Time: 4:00 - 5:30 PM EDT

Location: Chem 1706

For those who do not have access to gollum or would like to set up their own conda environment for pycharmm, clone this repo and create the conda environment by

cd pyCHARMM-Workshop/
conda create -n pyCHARMM -c conda-forge -c schrodinger \
pymol rdkit jupyterlab openbabel openmm
conda activate pyCHARMM

We will utilize pyCHARMM from the current developers stream. If you are working on gollum you can link to the pyCHARMM version I compiled using (tsch):

export CHARMM_HOME=/home/brookscl/charmm/c47-dev-release/
export CHARMM_LIB_DIR=$CHARMM_HOME/install-pycharmm-nompi/lib

Install pyCHARMM in the conda environment using pip

pip install $CHARMM_HOME/tool/pycharmm

If you are building pyCHARMM in your local environment (assuming Linux, gcc (I use v7.3), NVIDIA drivers (I use cuda v10.0)/gpu access with OpenMM already installed), in the CHARMM directory:

mkdir -p build_charmm; cd build_charmm
../configure --with-blade --with-fftdock --without-mpi \
--as-library -p ../install-pycharmm-nompi
make -j 2 -C install

Following this you will need to set the environment variable CHARMM_LIB_DIR as noted above to point to your install library directory, and install the pyCHARMM modules using pip.

pip install ../tool/pycharmm
export CHARMM_LIB_DIR=/path/to/charmm_dir/install-pycharmm-nompi/lib

1. MMTSB Toolset is utilized and should be installed .
2. propKa will be utilized.
3. pymol will be utilzied locally to view structures.

If you have pycharmm installed locally in the pyCHARMM virtual environment, you can start a jupyter-lab by typing jupyter lab in the same conda environment.

Introduction to CHARMM, how to build pyCHARMM and first steps in setting up molecular simulations with pyCHARMM, selecting atoms and basic manipulations of the PSF using pyCHARMM.

Setting up solvated molecular dynamics simulations, using OpenMM, BLaDE GPU accelerated simulation engines for molecular dynamics.

Using pyCHARMM CDOCKER for rigid-receptor, flexible ligand and flexible-receptor, flexible ligand docking.

Free energy simulations i) absolute solvation free energy calculations; ii) setting-up MSλD with msld-py-prep and pyCHARMM.

Advanced topics including integration of python tools with pyCHARMM, utilizing machine-learned potentials in pyCHARMM, parallelism in python with MPI.