Prepared input files for mup1, liga, bace, p38

[steinbt2]

Input submission checklist

• [ ] created a directory for each system based on the template directory
• [ ] named and placed the directory with the following pattern: input_structures/prepared_structures/<set_name>/<system_name>

For each submitted directory:

• [ ] filled in system preparation details in the PREPARATION_DETAILS.md file
• [ ] added a PDB file with the protein named protein.pdb
• [ ] removed any cofactors from the PDB file and placed them in cofactors.sdf
• [ ] did not re-protonate the residues, but left protonation state of the protein unchanged
• [ ] kept cystallographic waters and metals in the PDB file
• [ ] tested the PDB and, if available, cofactors.sdf file using the input validation script
• [ ] copied over the ligands SDF file to a file named ligands.sdf and removed any duplicate binding modes or protonation states, keeping the more favorable state

Summary of changes

Licensing agreement

• [ ] I agree to release these inputs under the combined MIT and CCBY SA 4.0 licenses of this repository

[hannahbaumann]

Thank you, @steinbt2 , this looks great! One small thing, could you add a bullet point to the preparation instructions for the BACE protein explaining the reason for removing the TLA, just for future reference? Thank you!

[steinbt2]

Here or should I make a new pull request?

TLA was presumed to be a crystalization buffer compound without functional relevance, surface-bound and far from the binding pocket.

[hannahbaumann]

Awesome, thank you! In this same PR would be perfectly fine!

[steinbt2]

I added and pushed a comment on the bace prep

[hannahbaumann]

Awesome, thanks! I'll go ahead and merge this PR!