QMrebind: Quantum Mechanical reparametrization at the receptor-ligand binding site

Release:

0.4.0

Date:

Oct 28, 2024

Molecular mechanics (MM) forcefields (FF) seek to approximate the potential energy surface (PES) of molecules in regions of phase space likely to be sampled in a realistic situation (for example: near equilibrium, in a biological context, etc.) While the FFs of common features, such as amino acids, are quite optimized, the parametrization of small molecules can be difficult and prone to errors. The QMrebind software automates the generation of parameters for small molecules in a context of interest - within the binding site, for instance. Therefore, a highly accurate PES is generated for the region of phase space where the ligand is in the bound state. The resulting parameters may be then used as input to subsequent calculations, such as SEEKR2.

Contents:

• About
  • Justification of the qmrebind project
• Installation
  • Install Conda
  • Install Orca
  • Install OpenMPI
  • Install XTB
  • Install QMrebind
• Quickstart
  • Input PDB file Requirements
  • Run QMrebind
• Tutorials for QMrebind
  • Tutorial: Running QMrebind on the HSP90 System
• Program Options
  • run_qmrebind_amber.py

Cite QMrebind

If you wish to cite QMrebind, please cite the following paper:

• Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci. 2023 Oct 24;14(45):13159-13175. doi: 10.1039/d3sc04195f. PMID: 38023523; PMCID: PMC10664576.

Getting Involved

Please report bugs or enhancement requests through the Issue Tracker.

Indices and tables

• Index

• Module Index

• Search Page