charmm-gui

Google Colab notebooks for running molecular dynamics simulations with GROMACS

Set up relative free energy calculations using a common scaffold

Automatic CHARMM-GUI browser interaction with Python

This code adds custom-made amino acids to the GROMACS forcefield directory.

Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

A multi-purpose tool for automated setup of MD systems (e.g. for transformato) and local, menu-based rerunning of CHARMM-GUI input scripts for CHARMM

Unofficial auditable workflow skill for CHARMM-GUI system building, recovery, and GROMACS package validation.

Analysis scripts for the CHARMM GUI Drude Prepper Paper

A Molecular Dynamics simulation project of pyrazinamidase studying its influence in antibiotic resistance of pyrazinamide. The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In GROMACS the fix shake command can be used to ho…

A reproducible, end-to-end computational pipeline that uses a machine-learning docking surrogate and receptor-aware fragment growing to design a new Nrf2-inhibitor candidate, followed by force-field parametrization, explicit-solvent energy minimization, and AI-assisted retrosynthetic assessment.

I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.

Scripts to help with setting up molecular dynamics simulations.

ASOs in LNPs with receptor-guided permeation