ChenGiuseppe / PyMM
A Python program for QM/MM Simulations based on the Perturbed Matrix Method
☆25Updated last year
Alternatives and similar repositories for PyMM:
Users that are interested in PyMM are comparing it to the libraries listed below
- ☆18Updated 3 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆28Updated 11 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 6 months ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆29Updated 2 months ago
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 4 years ago
- Code to accompany "Practical Cheminformatics With Open Source Software"☆16Updated 2 years ago
- Multiscale Simulation Tool for Backmapping☆16Updated this week
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆29Updated this week
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago
- ☆29Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 5 years ago
- Tautomer ratios in solution☆25Updated 3 years ago
- Fully automated docking pipeline (can be run in distributed environments)☆39Updated this week
- Cloud-based Drug Binding Structure Prediction☆34Updated 4 months ago
- Computational Chemistry Workflows☆54Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆43Updated 2 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆17Updated 2 years ago
- Standalone charge assignment from Espaloma framework.☆38Updated 6 months ago
- A collections of scripts for working molecular dynamics simulations☆41Updated 7 months ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆28Updated 4 years ago
- ☆19Updated 4 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 9 months ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- ☆25Updated last year
- ☆17Updated 11 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆21Updated 5 years ago