OFFICIAL: AnteChamber PYthon Parser interfacE
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Updated
Jul 15, 2024 - Python
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.
Framework for the rapid modeling glycans and glycoproteins.
A Package for Parametrization of Molecular Mechanics Force Fields
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.
Automatic CHARMM-GUI browser interaction with Python
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
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.
Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)
Parametrize a LAMMPS data file with a CHARMM force field
VMD plug-in for building a peptide ab initio from backbone torsion angles or secondary structure
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
Perform molecular dynamics experiments (MD) with NAMD on colab
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