charmm

There are 2 repositories under charmm topic.

• alanwilter / acpype

  OFFICIAL: AnteChamber PYthon Parser interfacE

  python3ambertoolsgromacsambermdcharmmcnsxplortopologies
  Language:Python 171

• Marcello-Sega / pytim

  a python package for the interfacial analysis of molecular simulations

  simulationsmolecular-dynamicsdata-analysismdanalysisgromacsnamdcharmmlammpsinterfacesscientific-computingwillard-chandlermolecular-simulationsmdtrajinterfacial-atomsopenmmpythonsasa
  Language:Python 76

• leelasd / OPLSAA-DB

  Database 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.

  molecular-dynamicsmolecular-simulationforce-fieldopls-aalammpsgromacsnamdcharmmtinkeropenmmthermodynamics
  31
• glycosylator

  tlemmin / glycosylator

  Framework for the rapid modeling glycans and glycoproteins.

  glycosylationglycoinformaticsglycan-structuresglycan-analysisglycanscharmmpythonglycosylator
  Language:Rich Text Format 28
• ParaMol

  JMorado / ParaMol

  A Package for Parametrization of Molecular Mechanics Force Fields

  parameterizationforcefield-parameterizationforcefieldambercharmm
  Language:Python 26
• dabble

  Eigenstate / dabble

  Membrane protein builder and parameterizer

  charmmamberpythonpsfgen
  Language:Rich Text Format 17

• HECBioSim / Longbow

  Longbow 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.

  high-performance-computingjob-submissionautomationscientific-computingpbs-protorquelsf-jobsslurmsgebioinformaticsbiosimulationmolecular-dynamicsgromacsamberlammpsnamdcharmmsupercomputerjob-schedulerjob-queue
  Language:Python 17

• cameronabrams / psfgen

  TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD

  charmmtclpdbpsfgenvmdnamdbashpythoncswig
  Language:Tcl 9
• addNewResidue.py

  kimjc95 / addNewResidue.py

  This code adds custom-made amino acids to the GROMACS forcefield directory.

  gromacsmolecular-dynamicsmolecular-dynamics-simulationcharmmcharmm-guiamberacpypesimulationmolecular-simulationmd-simulations
  Language:Python 8

• akaupang / macha

  A multi-purpose tool for automated setup of MD systems (e.g. for transformato) and local, menu-based rerunning of CHARMM-GUI input scripts for CHARMM

  bashcharmmcharmm-guipython3
  Language:Python 5

• nk53 / auto_cgui

  Automatic CHARMM-GUI browser interaction with Python

  charmmcharmm-guipython3splinter
  Language:Python 5

• fearlessroad / NAMD_to_CHARMM-GUI

  Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

  namdmolecular-dynamicscharmmcharmm-gui
  4

• arghya90 / CodeEntropy

  CodeEntropy is a python package and a collection of scripts that can be used to compute entropy using the multiscale-cell-correlation (MCC) theory from MD simulations.

  entropycharmmgromacspython3vibrational-entropiesmdprotein-entropy
  3

• stephanmg / topo-ff

  Parametrize a LAMMPS data file with a CHARMM force field

  lammpscharmmforce-fieldtcl
  Language:Perl 3

• tlemmin / peptideBuilder

  VMD plug-in for building a peptide ab initio from backbone torsion angles or secondary structure

  peptidescharmmvmdsecondary-structuretclpeptide-builder
  Language:Rich Text Format 1

• francescopatane96 / Molecular-dynamics-with-NAMD

  Perform molecular dynamics experiments (MD) with NAMD on colab

  bioinformaticsbiotechnologydynamicsmoleculardynamicssimulationcharmmisoformsmdminimizationmolecular-dynamicsmutantsnamdpdbproteindynamicssimulationequilibrationgroomacs
  Language:Jupyter Notebook 0

• mlnance / Lau_Lab_ALAD

  string-methodcharmmmolecular-dynamicsalanine-dipeptide
  Language:Python 0
• pepdroidff_materials_studio

  spheex / pepdroidff_materials_studio

  PEPDROID force field for peptoids

  peptoidforcefieldmaterialsstudioforcefieldnamdcharmmpdbmol2dreiding
  Language:Rich Text Format 0

• 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

  amberambertoolscharmmenergy-calculationsgmx-mmgbsagmx-mmpbsagromacsmd-simulationsmmgbsammpbsanamd
  Language:Python 0

• jo-sm / dcd

  CHARMM and X-PLOR binary trajectory file parser in Ruby

  charmmatomsdcdruby
  Language:Ruby

• meribold / mm-paper-trail

  :skull:

  charmmpandoc
  Language:GAP

• pierre-24 / just-psf

  Just get me a topology, for god’s sake!

  charmmpsftrajectory-analysis
  Language:Python