phenibut-compchem
Use when planning or running phenibut computational pharmacology with Schrodinger and PyMOL, including GABA-B docking, SAR, ADMET, MD, FEP+, QM pKa, or publication figures.
- License 许可
- MIT
- 最近更新
- 2026-11-02
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- ★ 0
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01 前言 Front Matter
- name
- phenibut-compchem
- metadata
- { "type": "project" }
- description
- Use when planning or running phenibut computational pharmacology with Schrodinger and PyMOL, including GABA-B docking, SAR, ADMET, MD, FEP+, QM pKa, or publication figures.
03 SKILL.md 正文
Phenibut Computational Pharmacology — Tool Routing & Pipeline
Companion to proof_empty/RESEARCH_PLAN.md and proof_empty/SCHRODINGER_TOOLKIT.md
(the authoritative capability map + gap analysis). Read those for the full module/feature detail.
Ground truth
- You own the full Schrodinger Drug Discovery Suite (2026-2, licensed to 2050): Glide, IFD/IFD-MD, FEP+, Desmond, Jaguar/QSite (QM), Prime+STA_GPCR, QikProp, Phase, SiteMap, WaterMap, Epik, MacroModel, Canvas, AutoQSAR, AutoDesigner. Buy nothing for the structural/chemistry layer.
- PyMOL 3.1.7 (Incentive) is the only figure tool. Headless:
Scripts\pymol.exe -cq script.pml. License lives at%USERPROFILE%\.pymol\license.lic(must be the real entitlement, not the auto-generated eval token — else figures get a watermark). - The mechanistic "why" questions (dopamine puzzle, withdrawal, prosocial effect) are neurobiology/systems pharmacology, not docking. Corpus synthesis + free tools (PK-Sim, STRING/Cytoscape, NEURON/Brian2) are the main engine; computation tests falsifiable sub-hypotheses.
MCP: schrodinger (server at C:\Users\agentuser\source\repos\schrodinger-mcp\server.py)
After editing the server, reconnect the MCP / restart Claude Code to reload it.
Tested, ready: schrodinger_version, backend_info, smiles_to_3d, molecule_properties,
convert_structure, ligprep, qikprop_admet, glide_grid, glide_dock, prepwizard,
prime_mmgbsa, run_schrodinger_python, pdb_fetch, qikprop_parse_results, pymol_render.
Standard structure-based pipeline (GABA-B + analogs)
Still needs an external install (no MCP covers it)
Gotchas
04 同仓库更多 Skills
clarify-requirements
Resolve genuine pre-execution ambiguity by scanning repo context, generating 1-6 grounded options, and asking 1-3 focused questions via AskUserQuestion. NOT for mid-task use (injection risk); NOT when the goal is already unambiguous; use to disambiguate vague prompts before any file edits.
openmm-md
Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein / protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.
visual-review
Take screenshots of web pages and UI using Playwright for visual review and iteration
status
Diagnostic status report — shows metaswarm installation state, project setup, and potential issues
start
Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work
setup
Interactive project setup — detects your project, configures metaswarm, writes project-local files