search

openmm / openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)
http://openmm.org
Other
258 stars 81 forks source link

AMBER: Append prefixes to atom types from protein, DNA, and RNA parameter sets #46

Closed jchodera closed 6 years ago

jchodera commented 6 years ago

See this comment and subsequent comments.

We have to decide whether to merge AMBER protein, DNA, and RNA parameters into a single file or append prefixes to all atom types from these files so they can be read in together.

jchodera commented 6 years ago

Per https://github.com/pandegroup/openmm/issues/1611#issuecomment-344998961, we are forced to add prefixes. AmberTools18 might merge these files instead.

To avoid the need to make extensive modifications to ParmEd to consistently add prefixes to atom types, we will modify the ffxml file directly using this ugly hack suggested by @peastman.

We will also need to test the updated file, and ideally also test that multiple files (proteins, DNA, RNA) can be included together.

jchodera commented 6 years ago

This is addressed in https://github.com/choderalab/openmm-forcefields/pull/51