https://github.com/insilichem/tangram_mmsetup

A graphical interface to run OpenMM simulations in UCSF Chimera.
https://github.com/insilichem/tangram_mmsetup

molecular-dynamics openmm ucsf-chimera

Last synced: about 1 month ago
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A graphical interface to run OpenMM simulations in UCSF Chimera.

• Host: GitHub
• URL: https://github.com/insilichem/tangram_mmsetup
• Owner: insilichem
• Created: 2017-11-06T12:37:47.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-02-01T17:46:57.000Z (almost 6 years ago)
• Last Synced: 2023-10-20T20:24:08.356Z (about 1 year ago)
• Topics: molecular-dynamics, openmm, ucsf-chimera
• Language: Python
• Homepage: http://tangram-suite.readthedocs.io/en/latest/tangram_mmsetup.html
• Size: 117 KB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
# Tangram MMSetup

A graphical interface to run OpenMM simulations in UCSF Chimera.

# Dependencies

This extension relies on [ommprotocol](https://github.com/insilichem/ommprotocol), which in turn depends on OpenMM, PDBFixer, MDTraj, ParmEd, OpenMolTools and some more. All of these requirements should be handled by the main [Tangram installer](https://github.com/insilichem/tangram).

# Quick Usage

1. Open any molecule on UCSF Chimera

2. Click on `Sanitize` to fix common problems with PDB files.

3. Add a new stage for the simulation. `ommprotocol` is designed to run all the steps of a MD protocol in the same job, saving you from the effort of chaining output and input files for each stage. However, in trivial cases, a single stage with minimization is enough.

4. Finally, the interface can be used for two different purposes:

    - Clicking on `Run`, OMMProtocol will be launched within UCSF Chimera with realtime coordinates updating (useful for teaching, for example).

    - Clicking on `Save Input`, an OMMProtocol input file (.yaml) will be generated so you can run `ommprotocol` separately (suitable for long runs in cluster computers).