drug-complex-system-builder
drug-complex-system-builder is a Chemistry & materials skill for AI agents, published by learningmatter-mit in the AtomisticSkills repository on GitHub. Skillspace rates drug-complex-system-builder D (69/100) and it passed the safety scan; the rating is based on static analysis only.
Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation. Combines a prepared receptor PDB and ligand SDF, parameterizes the ligand with OpenFF Sage or GAFF (AM1-BCC charges), applies Amber ff14SB to the protein, solvates with explicit water, and adds counterions. Use this skill when the user wants to solvate a complex, set up a system for MD, prepare for simulation, add water and ions, or build a simulation box from a protein-ligand structure.
- Grade
- D
- Quality
- 69 / 100
- Safety
- Passed
- GitHub stars
- 132
Unproven: rated by static analysis only, not yet compared head-to-head.
This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.
Our review
- Architecture
- 78 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- No issues found
- License
- MIT
- Adoption
- Adopted by 0 other repositories, in 0 collections
Not checked yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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