Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L

2020-02-22T08:56:48Z (GMT) by J. Vreede Sander Roet David Swenson

This is the data and scripts to reproduce the kras data, after unpakcing all tar files.

1. Install the conda environment "kras.env"

2. pip install openpathsampling to commit 78382fce67f99f4d160c01673d5553affebb2437 (also listed in the comment at the top of kras.env)

3. Make sure that you set the shell environment variables needed for the OpenMM platform you intend to use.

4. Go into the directory you want to simulate.

5. Alter the "make_engine" function in the .py file to fit your OpenMM platform, see http://docs.openmm.org/latest/userguide/library.html

5.a Point the "includeDir='/home/10166149/top" to the "top" directory in this directory

6. Call the python file with the flags "-nc init_traj.nc -snc states.nc -ts total_MC_steps"

for instance to do 1000 steps for Q61L/switch1

./run_tps.py -nc init_traj_S1_Q61L.nc -snc states_TPS_S1_Q61L.nc -ts 1000