WaSiMap - Test Data

WaSiMap - MD Test Data This repository contains the test data for the WaSiMap water-site mapper software, consisting of three MD simulations of the ABL1-3bp1 complex. Two such simulations are in H5 format (sim1 and sim2), and the remaining simulation (sim3) in .NC format, with its corresponding Amber topology file in PRMTOP format. The simulation "sim1" contains the wild-type complex, whereas "sim2" and "sim3" contain interfacial amino acid mutations (p3 and p4). These files can be downloaded manually by the end-user and deposited in a folder, or automatically using the wasimap CLI command with the flag --testdata The simulation time is 2ns in 1000 frames All simulations contain explicit TIP3P water The total size of all files is 320MB The purpose of these simulations is to serve as example to showcase the cappabilities of WaSiMap in exctracting and visualizing water-site information. Archived folder "S1 Data.zip" contains the templates, MD input files, scripts and settings that were used to run the MD simulations with OpenMM. For further details on how these simulations were created, refer to the supplementary data S1 Appendix of the WaSiMap manuscript.