The structural files and scripts to launch ATM calculation on Schindler et al. dataset.
The repository is organized as following:
Under the targets directory, the repo includes 8 different target systems: cdk8, cmet, eg5, hif2a, pfkfb3, shp2, syk, tnks2.
Inside each target, the repo provides:
- edges_analysis.csv (ATM results for each pair)
- free_energy/pairname
- atom.cntl (ATM control file).
- mintherm_atm.py/mdlambda_equil_atm.py/mdlambda_atm.py (ATM structural equilibration protocol).
- complex.prmtop/complex.inpcrd (molecular system for each pair).
- nodefile (file that specifies available GPU devices).
Under the scripts directroy, the repo provides two useful scripts:
- run_atm.sh (script to run ATM calculation for each RBFE pair).
- uwhat_analysis.R (script to analyze perturbation with UWHAT).