We recommend going over the tutorials in this sequence.
- ABFE/temoa-g1: absolute binding free energy between the TEMOA host and the G1 guest from the SAMPL8 GDCC challenge.
- RBFE/temoa-g1-g4: relative binding free energy between the G1 and G4 guests to the TEMOA host from the SAMPL8 GDCC challenge.
- ABFE/fkbp: absolute binding free energies of a series of complexes of FKBP with ligand fragments from Pan A, Xu H, Palpant T, Shaw DE; JCTC 2017
- RBFE/eralpha: relative binding free energies of four ligands binding to the ERα protein receptor from Azimi, Khuttan, Wu, Pal, Gallicchio. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method.
- RBFE/cdk2: relative binding free energies of six CDK2 inhibitors from Wang et al. (2013) Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors
This AToM-OpenMM software. The examples have been written assuming that it is installed under $HOME/software/AToM-OpenMM.
Follow the installation instructions to install OpenMM and the ATM Meta Force plugin. In general, we assume that the OpenMM libraries (version 7.6.0 or newer) have been installed in a location where python can find them. Presumably you did so under a conda environment. If so activate the environment to run the examples. We also assume that the ATMMetaForce OpenMM plugin is installed and available within the same OpenMM environment and that python can find the corresponding python bindings.
When using a conda environment, the examples can be launched with the python command of that environment. For other situations, a sample runopenmm script is provided in the scripts/ to get you started if needed. It requires you to define the environment variable OPENMM_DIR pointing to the OpenMM installation on your system. It also assumes that the python OpenMM bindings have been stored under the same folder.
Free energy analysis requires R with the UWHAM R module. Do conda install r-base to install R in a conda environment. To install the UWHAM module run install.packages("UWHAM") in R.