GilsonLabUCSD / pAPRikaLinks
Advanced toolkit for binding free energy calculations
☆33Updated 3 months ago
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
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 6 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Package for consistent reporting of relative free energy results☆40Updated last week
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆15Updated this week
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆71Updated last month
- Set up relative free energy calculations using a common scaffold☆24Updated 4 months ago
- Standalone charge assignment from Espaloma framework.☆45Updated 2 months ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated 9 months ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- ☆22Updated 3 years ago
- ☆30Updated last week
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆40Updated last year
- An automated framework for generating optimized partial charges for molecules☆39Updated last month
- Physical validation of molecular simulations☆57Updated 2 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆80Updated last week
- ☆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
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated 5 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated last year
- A Package for Parametrization of Molecular Mechanics Force Fields☆32Updated 3 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆42Updated last year
- User Guide for MDAnalysis☆29Updated this week
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Repository for the 2024 OpenFE industry benchmark efforts☆28Updated 2 months ago
- OpenFF NAGL☆19Updated last week
- Dihedral scanner with wavefront propagation☆36Updated 7 months ago
- Comparison benchmarks between public force fields and Open Force Field Initiative force fields☆10Updated 3 years ago