Amber-MD / pytraj

Related projects: ⓘ

• jensengroup / propka
  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
  ☆258Updated 7 months ago
• choderalab / yank
  An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
  ☆177Updated last year
• openforcefield / openff-toolkit
  The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…
  ☆309Updated this week
• alanwilter / acpype
  OFFICIAL: AnteChamber PYthon Parser interfacE
  ☆196Updated this week
• choderalab / pymbar
  Python implementation of the multistate Bennett acceptance ratio (MBAR)
  ☆235Updated 3 weeks ago
• Becksteinlab / GromacsWrapper
  GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
  ☆169Updated this week
• openmm / openmmforcefields
  CHARMM and AMBER forcefields for OpenMM (with small molecule support)
  ☆249Updated last month
• choderalab / openmmtools
  A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
  ☆245Updated last week
• Amber-MD / cpptraj
  Biomolecular simulation trajectory/data analysis.
  ☆134Updated 2 weeks ago
• Acellera / htmd
  HTMD: Programming Environment for Molecular Discovery
  ☆255Updated 2 weeks ago
• jalemkul / gmx_tutorials_livecoms
  LiveCoMS GROMACS Tutorials Paper
  ☆105Updated 5 years ago
• Valdes-Tresanco-MS / gmx_MMPBSA
  gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
  ☆215Updated 4 months ago
• deGrootLab / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆131Updated last month
• alchemistry / alchemlyb
  the simple alchemistry library
  ☆191Updated this week
• Acellera / moleculekit
  MoleculeKit: Your favorite molecule manipulation kit
  ☆198Updated last week
• Colvars / colvars
  Collective variables library for molecular simulation and analysis programs
  ☆201Updated this week
• MobleyLab / basic_simulation_training
  A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …
  ☆109Updated 5 years ago
• MobleyLab / alchemical-analysis
  An open tool implementing some recommended practices for analyzing alchemical free energy calculations
  ☆113Updated 3 months ago
• tubiana / TTClust
  clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
  ☆104Updated 4 months ago
• MobleyLab / drug-computing
  Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by…
  ☆141Updated 6 months ago
• chemosim-lab / ProLIF
  Interaction Fingerprints for protein-ligand complexes and more
  ☆355Updated 3 weeks ago
• openmm / pdbfixer
  PDBFixer fixes problems in PDB files
  ☆461Updated last month
• GrossfieldLab / loos
  LOOS: a lightweight object-oriented structure analysis library
  ☆121Updated last week
• molmod / openmm-tutorial-msbs
  OpenMM tutorial for the MSBS course
  ☆141Updated this week
• mittinatten / freesasa
  C-library for calculating Solvent Accessible Surface Areas
  ☆107Updated 3 months ago
• Electrostatics / pdb2pqr
  PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
  ☆124Updated 6 months ago
• rdkit / rdkit-tutorials
  Tutorials to learn how to work with the RDKit
  ☆254Updated last year
• mdtraj / mdtraj
  An open library for the analysis of molecular dynamics trajectories
  ☆584Updated this week
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆94Updated last week
• Discngine / fpocket
  fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…
  ☆283Updated last week