Input files for "Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations"

Supporting Information for:

• S. Bhusal and O. Valsson
  Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations
  ChemRxiv Preprint, submitted to Phys. Chem. Chem. Phys. (2025)
  ChemRxiv: 10.26434/chemrxiv-2025-bxf47

This archive contains input files used to generate the data.

Authors

Shikshya Bhusal - [email protected]
Department of Chemistry
University of North Texas
Denton, Texas, USA
ORCID: 0000-0001-5668-645X

Omar Valsson - [email protected]
Department of Chemistry
University of North Texas
Denton, Texas, USA
ORCID: 0000-0001-7971-4767
Website: www.valsson.info

Software

Files were run with the following codes:

• GROMACS 2022.5 MD code
• PLUMED 2.8.2 enhanced sampling plug-in code
• VMD 1.9.3 for trajectory analysis

File Overview:

• All the .gro, .itp and .top files for each solvent are located in their respective folders under Input_Files
  • Water: Input_Files/Water
  • Chloroform: Input_Files/Chloroform
  • DMSO: Input_Files/DMSO
• The GROMACS molecular dynamics parameters can be found in the md-npt.mdp file.
• The DMSO and chloroform simulations were run with the -tunepme no flag to disable the PME parameter tuning at run time.
• The Parallel Bias Metadynamics simulations are run using the following PLUMED input files:
  • plumed_pbmetad.dat: include all CVs defined in the simulations and the PBMetaD bias.
• The last bias reweighting post-processing was run using the plumed driver using the following PLUMED input files:
  • plumed_lastbias.dat
  • plumed_read.dat: used to read from files the relevant CVs for the reweighting

License

Copyright (c) 2025 Shikshya Bhusal and Omar Valsson

Creative Commons Attribution 4.0 International Public License (CC BY 4.0). See LICENSE for more details.