SAMPL9 blind predictions using nonequilibrium alchemical approaches
Piero Procacci, Guido Guarnieri · Zenodo (CERN European Organization for Nuclear Research) · 2022
Data from "SAMPL9 blind predictions using non-equilibrium alchemical approaches" Submitted to J Comput Aided-Mol Des, January 2022. traj -> This directory contains trajectory files for SAMPL9: g??_w.pdb.gz file contains ~ 100 snapshots from the 48 ns HREM sampling of the target bound state of G1-G18 including water solvent. g??_1.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the g??_16.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the hottest bound state of G1-G18 target bound state of G1-G13 work -> This trajectory contains the work data (in kJ/mol) obtained in the NE trajectories for SAMPL9: g??_b_TIME.wrk is the work sample obtained when annihilating the ligand in the bound state with a duration time of TIME. g??_u_TIME.wrk is the work sample obtained when growing the ligand in the bulk solvent state with a duration time of TIME. g??_b_TIME.qwrk is the work sample for discharging the ligand in the bound state g??_u_TIME.qwrk is the work sample for recharging the ligand in the bulk solvent state pdb -> This directory contains the pdb initial structures of the G1-G18 guests and the WP6 host ff -> This directory contains the force field specification for SAMPL9: the PrimaDORAC generated (http://www1.chim.unifi.it/orac/primadorac/) tpg and prm files for the guests and the host in orac format. (see http://ftp.chim.unifi.it/orac/MAN/orac-manual.html) inputs-> This directory contains the input files (in the g?? dirs) for launching the HREM simulation on a HPC cluster. A brief tutorial can be found in the README file