byun-jinyoung / atm_merckset

The structural and input files for ATM RBFE on Mecrk Dataset

Description

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).