Valdes-Tresanco-MS/gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Language: Python - Size: 330 MB - Last synced at: about 22 hours ago - Pushed at: about 22 hours ago - Stars: 265 - Forks: 72

alanwilter/acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

Language: Python - Size: 287 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 229 - Forks: 53

hopanoid/Enzyme-Reaction-Dynamics-Tutorial

A QM-MM Tutorial of Enzyme Reaction Dynamics

Language: Shell - Size: 9.95 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 1

AspirinCode/AlphaPPImd

Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks

Language: Jupyter Notebook - Size: 7.98 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 28 - Forks: 3

Amber-MD/pytraj

Python interface of cpptraj

Language: Jupyter Notebook - Size: 526 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 176 - Forks: 38

crfield18/PhD-scripts

A collection of scripts written for use with different computational biology/chemistry packages throughout my PhD.

Language: Python - Size: 104 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

suleymanselim/AmberTutorials

Language: Shell - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

xBFreEnergy/xBFreE

xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs

Language: Python - Size: 32.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kzinovjev/sqm-am1-dhfr

AM1 specific reaction parameters for DHFR catalyzed reaction in sqm (AmberTools18)

Language: Fortran - Size: 146 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

aretasg/amber-emm

Python utility script to perform energy minimisation on a small molecule PDB file using AmberTools

Language: Python - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

xBFreEnergy/xBFreEnergy.github.io

Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

yylonly/AmberDocker

Amber docker images for molecular dynamics

Language: Shell - Size: 301 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 2

mackevinbraza/WE-fl-A3B

Collections of files and tools for weighted ensemble simulations of full-length APOBEC3B

Language: Jupyter Notebook - Size: 3.91 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

GoHypernet/Galileo-AmberTools-Framework

Repository for AmberTools Mission framework type in Galileo.

Language: Dockerfile - Size: 373 KB - Last synced at: 7 days ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1