williamdlees / AmberUtils
Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods
☆20Updated 5 years ago
Alternatives and similar repositories for AmberUtils:
Users that are interested in AmberUtils are comparing it to the libraries listed below
- Collection of Python scripts to setup and run simulations with OpenMM☆15Updated 4 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 3 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆28Updated 9 months ago
- Analysis of non-covalent interactions in MD trajectories☆53Updated 2 months ago
- ☆18Updated 3 years ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆19Updated 3 years ago
- ☆25Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- RF-Score-VS binary☆30Updated 6 years ago
- ☆26Updated 9 months ago
- ☆28Updated last year
- Parallelized Open Babel & Autodock suite Pipeline☆23Updated 6 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 7 months ago
- ☆55Updated last year
- Computational Chemistry Workflows☆54Updated 2 years ago
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆32Updated 11 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆27Updated 3 years ago
- Python code for generating Boresch restraints from MD simulations☆19Updated 2 years ago
- Fully automated docking pipeline (can be run in distributed environments)☆42Updated last month
- A collections of scripts for working molecular dynamics simulations☆42Updated 9 months ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆27Updated 8 months ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- Trusted force field files for gromacs☆45Updated 4 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆13Updated last year
- MD pharmacophores and virtual screening☆33Updated last year
- a VMD plugin for binding affinity prediction using end-point free energy methods☆28Updated 8 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- The public versio☆47Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 6 months ago