alanwilter / acpype
OFFICIAL: AnteChamber PYthon Parser interfacE
☆226Updated 3 months ago
Alternatives and similar repositories for acpype:
Users that are interested in acpype are comparing it to the libraries listed below
- the simple alchemistry library☆213Updated 4 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆188Updated last year
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆254Updated last month
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆293Updated last year
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆289Updated this week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆144Updated 2 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆143Updated 3 weeks ago
- Interface for AutoDock, molecule parameterization☆250Updated this week
- Describe and apply transformation on molecular structures and topologies☆112Updated this week
- Force fields produced by the Open Force Field Initiative☆149Updated 2 weeks ago
- LiveCoMS GROMACS Tutorials Paper☆115Updated 5 years ago
- OpenMM tutorial for the MSBS course☆161Updated last week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆197Updated 2 months ago
- tools for GROMACS☆110Updated 3 weeks ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆185Updated last year
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆72Updated 8 months ago
- binding free energy estimator 2☆113Updated last week
- Visual Interactive Analysis of Molecular Dynamics☆287Updated last week
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆344Updated 7 months ago
- Scoring of shape and ESP similarity with RDKit☆214Updated last month
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆112Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆132Updated last month
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆127Updated 11 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆250Updated last month
- Some useful RDKit functions☆169Updated last month
- Python interface of cpptraj☆176Updated 3 months ago
- Interaction Fingerprints for protein-ligand complexes and more☆408Updated this week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆271Updated this week
- Auto3D generates low-energy conformers from SMILES/SDF☆167Updated last month
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆231Updated this week