fjclark/bss_multiple_distance_restraints_example

Example scripts and inputs for running an ABFE calculation with multiple distance restraints through BioSimSpace

Example Scripts and Inputs to Run an ABFE Calculation with Multiple Distance Restraints

This uses BioSimSpace to prepare the calculation and select the restraints, and SOMD to run the ABFE calculations. Note that this currently only runs the bound leg of an ABFE calculation. SLURM is used for job submission.

Requirements

• Custom version of Sire available here. Follow the instructions to install from source, making sure to install the BioSimSpace dependencies. Make sure to check out the correct branch before installing (feature_permanent_mdr).
• Custom version of BioSimSpace available here. Follow the instructions to install from source. Make sure to check out the correct branch before installing (feature_mdr).

Customising Input/ Scripts

To allow the calculation to run for your system on your cluster:

• Edit the SLURM options in the slurm_run.sh and slurm_analysis.sh scripts to match your cluster.
• Replace the SYSTEM.rst7 and SYSTEM.prm7 files in the input directory with your own equilibrated input files. Add a trajectory (of the fully interacting complex) file called "traj.dcd" to allow the restraint to be selected. Ensure that your ligand is named LIG.

Running the Calculation

Create a calculation directory and move into it:

mkdir calculation
cd calculation

From the calculation directory, run:

python ../scripts/run_abfe_bound.py

To use Boresch restraints instead, run:

python ../scripts/run_abfe_bound.py -rt boresch

If you are running from a different relative path, or have renamed/ moved some of the scripts or inputs, you will have to specify this. Run python ../scripts/run_abfe_bound.py --help for details.