GilsonLabUCSD / pAPRikaLinks
Advanced toolkit for binding free energy calculations
☆33Updated last month
Alternatives and similar repositories for pAPRika
Users that are interested in pAPRika are comparing it to the libraries listed below
Sorting:
- RESP with inter- and intra-molecular constraints in Psi4.☆32Updated 2 years ago
- Package for consistent reporting of relative free energy results☆40Updated this week
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆33Updated 4 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆70Updated 2 weeks ago
- Standalone charge assignment from Espaloma framework.☆41Updated 2 weeks ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆78Updated 2 weeks ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated last week
- OpenFF NAGL☆18Updated 2 weeks ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- ☆30Updated 2 months ago
- This package contains tools for setting up hybrid-topology FE calculations☆32Updated 2 weeks ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated 7 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 10 months ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆30Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆61Updated last year
- An automated framework for generating optimized partial charges for molecules☆39Updated 2 weeks ago
- ☆44Updated 3 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- OpenMM plugin to interface with PLUMED☆68Updated 7 months ago
- A Package for Parametrization of Molecular Mechanics Force Fields☆33Updated 2 years ago
- User Guide for MDAnalysis☆27Updated 2 weeks ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆22Updated 3 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Dihedral scanner with wavefront propagation☆34Updated 5 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆27Updated 5 years ago