David Minh

Use Open Force Field parameters for ligands

20

There is no clear way to use Open Force Field parameters for ligands, as the YAML input takes in mol2 and leaprc.gaff. Maybe if the ligands could be set up...

If you want to incorporate a binding pose prediction into YANK, this code that I wrote today could be a helpful reference. This extracts the bound state and aligns it:...

mpi4py should be a dependency of conda installer

3

I got this error from a fresh install from miniconda3 when running on XSEDE Bridges. Traceback (most recent call last): File "/home/dminh/.conda/envs/yank/bin/yank", line 11, in load_entry_point('yank==0.25.2', 'console_scripts', 'yank')() File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/cli.py",...

Ensembler assumes that UniProt sequences can be refined by a "domain", but not all UniProt sequences are associated with a domain. Right now, ensembler treats these domains as not existing....

Pin msmbuilder version to 3.3.1 until API can be updated

1

I get this error: ``` Constructing a trajectory containing all valid models... Conducting RMSD-based clustering... Traceback (most recent call last): File "/share/apps/anaconda/2/bin/ensembler", line 6, in sys.exit(ensembler.cli.main()) File "/share/apps/anaconda/2/lib/python2.7/site-packages/ensembler/cli.py", line 40,...