alanwilter / acpypeLinks
OFFICIAL: AnteChamber PYthon Parser interfacE
☆245Updated 3 weeks ago
Alternatives and similar repositories for acpype
Users that are interested in acpype are comparing it to the libraries listed below
Sorting:
- Describe and apply transformation on molecular structures and topologies☆139Updated 3 weeks ago
- the simple alchemistry library☆232Updated 3 weeks ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆166Updated 2 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Updated 2 weeks ago
- LiveCoMS GROMACS Tutorials Paper☆138Updated 6 years ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆348Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆205Updated 2 years ago
- OpenMM tutorial for the MSBS course☆183Updated 2 weeks ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆334Updated 2 weeks ago
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆126Updated last year
- Force fields produced by the Open Force Field Initiative☆176Updated last month
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆295Updated 2 months ago
- binding free energy estimator 2☆137Updated 3 weeks ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆185Updated 5 months ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆135Updated last year
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆182Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆152Updated 3 weeks ago
- Visual Interactive Analysis of Molecular Dynamics☆317Updated this week
- Scoring of shape and ESP similarity with RDKit☆232Updated 5 months ago
- Auto3D generates low-energy conformers from SMILES/SDF☆187Updated 3 weeks ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Updated 2 years ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆219Updated 2 weeks ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆381Updated 3 weeks ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆167Updated last month
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆162Updated last week
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆216Updated last year
- Benchmark set for relative free energy calculations.☆119Updated last year
- tools for GROMACS☆139Updated 7 months ago
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆204Updated last year
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆76Updated last year