OFFICIAL: AnteChamber PYthon Parser interfacE

a python package for the interfacial analysis of molecular simulations

Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.

A Package for Parametrization of Molecular Mechanics Force Fields

Framework for the rapid modeling glycans and glycoproteins.

Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.

Membrane protein builder and parameterizer

Self explained tutorial for molecular dynamics simulation using gromacs

Automatic CHARMM-GUI browser interaction with Python

TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD

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

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

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

CodeEntropy is a python package and a collection of scripts that can be used to compute entropy using the multiscale-cell-correlation (MCC) theory from MD simulations.

Parametrize a LAMMPS data file with a CHARMM force field

Just get me a topology, for god’s sake!

VMD plug-in for building a peptide ab initio from backbone torsion angles or secondary structure

Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic discovery.

Files used for the results presented in my physics undergraduate thesis.

xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs