32 skills found · Page 1 of 2
openmm / OpenmmforcefieldsCHARMM and AMBER forcefields for OpenMM (with small molecule support)
alanwilter / AcpypeOFFICIAL: AnteChamber PYthon Parser interfacE
tubiana / TTClustclusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
Marcello-Sega / Pytima python package for the interfacial analysis of molecular simulations
BrooksResearchGroup-UM / PyCHARMM WorkshoppyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.
Lemkul-Lab / Cgenff Charmm2gmxPython scripts to convert CGenFF stream files to GROMACS format
pritampanda15 / Molecular DynamicsSelf explained tutorial for molecular dynamics simulation using gromacs
leelasd / OPLSAA DBDatabase of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
tlemmin / GlycosylatorFramework for the rapid modeling glycans and glycoproteins.
JMorado / ParaMolA Package for Parametrization of Molecular Mechanics Force Fields
quantaosun / NotebookMy first ever repository, some notebooks useful, others sucks. Topics include file format conversion with obabel, docking with Auto Dock, MD with Charmm GUI and QSAR etc, never expect the format is perfect.
RagnarB83 / Chemshell QMMM Protein SetupMM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshell) and the ORCA code as QM code for Chemshell.)
Sumangal44 / Charmmono Theme🚀👨🏭❤️Charmmono-Theme is a sleek VS Code theme inspired by monospace aesthetics and Charmed Icons, offering a minimal, elegant, and highly readable coding experience with dark & light modes. 🚀
hendrikheinz / INTERFACE Force Field And Surface ModelsA force field for the simulation of inorganic-organic interfaces (INTERFACE-CHARMM, INTERFACE-PCFF)
Eigenstate / DabbleMembrane protein builder and parameterizer
OmarArias-Gaguancela / MD Quick PlotMD_quick_plot helps you plot MD simulation data figures using structural and trajectory files. Compatible formats include GROMACS, AMBER, CHARMM, and NAMD.
nk53 / Auto CguiAutomatic CHARMM-GUI browser interaction with Python
HECBioSim / LongbowLongbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.
leelasd / OPLS AAMImplementing OPLS-AA/M Force field in OpenMM from CHARMM formatted parameter files
kimjc95 / AddNewResidue.pyThis code adds custom-made amino acids to the GROMACS forcefield directory.
