therealchrisneale

8 processes works OK: While running mpiexec.hydra -np 8 yank script --yaml=p-xylene-implicit.yaml: bash-4.2$ free total used free shared buff/cache available Mem: 131934588 5161320 114950568 1014712 11822700 124444344 Swap: 0 0...

Hello, I find that the following command takes 4 minutes to get to the point of “execute _propagate_replica(0)” but then produces no more output while still consuming CPU resources for...

Hello, I see carriage returns in some database input files: $ ./alphafold/scripts/download_pdb_seqres.sh TEST $ grep -r $'\r' TEST/pdb_seqres/pdb_seqres.txt | wc -l 1476032 Should I remove them (e.g., sed -i "s/\r$//"...

This is a feature request ## Issue Information $ LigParGen -h usage: LigParGen [-h] [-r RESNAME] [-s SMILES] [-m MOL] [-p PDB] [-o {0,1,2,3}] [-c {0,-1,1,-2,2}] [-l] Ligand Parameter Generator...

- This is a feature request to allow BOSSdir to be longer than 80 characters. Not sure if the issue is in BOSS or LigParGen (command-line version) ## Issue Information...

- I believe this to be either a bug with LigParGen (command-line version only), or perhaps the online webserver is doing additional preparatory steps that I have not included for...

environment.yaml pulls new versions of packages that probably don't work together with this code

6

Is it possible to provide a list of package versions that once worked and can now be pinned? I find that the scripts here are not working and I am...

The current git repo seems inconsistent. I understand from searching tickets that some targets have been removed (e.g., https://github.com/openforcefield/protein-ligand-benchmark/issues/31). But some of the meta data doesn't reflect those updates, which...

sulfate angle parameters are incorrectly identified

3

**Describe the bug** When attempting to parameterize a sulfate smiles of "[O-]S(=O)(=O)[O-]", the resulting topology does not assign all angles to 109.5 degrees. **To Reproduce** ``` import openmm from openff.toolkit...