Summary

This is a collection of the input files for 8 protein-ligand systems (552 ligand perturbations): cdk8, cmet, eg5, hif2a, pfkfb3, shp2, syk, tnks2.

Citation:

Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, and Bert L. de Groot. Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. 2022. doi.org/10.1021/acs.jcim.1c01445

Folder structure:

For every protein-ligand dataset

- ligands_gaff2: for every ligand two topology files are present. 
ffMOL.itp contains the atomtypes, the rest of topology parameters are in MOL.itp. 
Structure is in the mol_gmx.pdb file. Force field: Gaff v2.11

- ligands_cgenff: topology and structure for cgenff. 
CGenFF v3.0.1 with the atom typing based on MATCH was used.

- ligands_openff: topology and structure for OpenFF. 
OpenFF 1.2.0 Parsley

- protein_amber: structure and topology for protein and, 
if available, co-crystallized waters and ions. Force field: amber99sb*ILDN

- protein_charmm: structure and topology for Charmm36m force field

- transformations_gaff2: edge information and hybrid structures/topologies for gaff2.

- transformations_cgenff: edge information for cgenff. 

- transformations_openff: edge information for OpenFF. 

ddg_data: the folder contains calculated ddG values for all the protein-ligand datasets

mdp: simulation parameter files

  - em_l0.mdp and em_l1.mdp: energy minimization for the states A and B
  - eq_nvt_l0.mdp and eq_nvt_l1.mdp: 100 ps NVT equilibration for the states A and B
  - eq_l0.mdp and eq_l1.mdp: 6 ns equilibrium run for the states A and B
  - ti_l0.mdp and ti_l1.mdp: 50 ps transition A->B and B->A.