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#8699 closed enhancement (fixed)
Add OpenMM ligand parameterization for tug and minimize mouse modes
| Reported by: | Tom Goddard | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | MD/Ensemble Analysis | Version: | |
| Keywords: | Cc: | Elaine Meng, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Currently the tug and minimize mouse modes only handle standard amino acids, nucleic acids, water, some ions and a very limited set of ligands. Nigel Moriarty calculated Amber parameters for most of the PDB ligands in 2019 and those are used in ISOLDE to run OpenMM simulations. Would be nice to use those with the tug and minimize mouse modes.
Change History (2)
comment:1 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
comment:2 by , 3 years ago
| Cc: | added |
|---|
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Done. In ChimeraX 1.6 and daily builds newer than March 23, 2023.
If the TugLigands Toolshed bundle is installed then the tug and minimize mouse modes will handle 21471 ligands based on their PDB 3-letter codes. I made this a Toolshed bundle because the ligand parameters are 25 Mbytes compressed and most people will not use them so I did not want to increase the size of the ChimeraX distribution. More details are on the Toolshed