Tangram MMSetup

A graphical interface to run OpenMM simulations in UCSF Chimera.

Dependencies

This extension relies on 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.

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).