Description of deposited MD files

This repository contains the molecular dynamics input files and topology files for the Hsp90β WT and Hsp90β T446E systems described in the associated manuscript.

The repository is organized into two main folders:

• Hsp90-beta

• Hsp90-beta-T446E

These folders correspond to the two simulated systems: the wild-type Hsp90β system and the T446E mutant system.

Folder: Hsp90-beta

This folder contains the input files for the Hsp90β WT simulations.

It includes:

• Hsp90-beta.ATP.WT.solv.prmtop
  Amber topology file for the solvated Hsp90β WT system in complex with ATP.

• starting_min.rst
  Minimized starting structure common to the three independent replicas before equilibration.

• replica-1, replica-2, replica-3
  Each replica folder contains the final structure obtained after the equilibration protocol. This structure corresponds to the starting structure used for the corresponding production MD simulation.

Folder: Hsp90-beta-T446E

This folder contains the input files for the Hsp90β T446E simulations.

It includes:

• Hsp90-beta.ATP.T446E.solv.prmtop
  Amber topology file for the solvated Hsp90β T446E system in complex with ATP.

• starting_min.rst
  Minimized starting structure common to the three independent replicas before equilibration.

• replica-1, replica-2, replica-3
  Each replica folder contains the final structure obtained after the equilibration protocol. This structure corresponds to the starting structure used for the corresponding production MD simulation.

Notes

For both systems, three independent replicas were generated. The minimized structure provided in the main system folder was used as the common starting point for the equilibration stage. The final equilibrated structure deposited in each replica folder was then used as the initial structure for the corresponding production MD simulation.

The deposited files are intended to document the molecular systems and starting configurations used for the MD simulations reported in the manuscript.