Amber chemist

Skill scaliaven/chemist/amber-chemist

Claude Code skills for computational chemistry — orchestrating atomistic simulations and molecular dynamics from natural language

Install

npx -y skills add scaliaven/chemist --skill amber-chemist

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One thing to look at

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What its author says it does

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Use this skill whenever the user wants to run, set up, restart, extend, or replicate Amber-native molecular dynamics — single-replica or replica-exchange — on small organics in explicit or implicit solvent. After the MD finishes, this skill also drives cpptraj-based analysis (RMSD/RMSF/RDF/hbond/radgyr, per-frame energy decomposition via esander) and MMPBSA-style endpoint scoring (MMPBSA / MMGBSA, alanine scan, per-residue decomposition) as add-ons that consume the MD output. MD-core trigger phrases — "Amber MD", "production NPT in pmemd", "1 ns of explicit-solvent MD", "Berendsen barostat", "Monte Carlo barostat", "Langevin thermostat at gamma_ln", "extend my prod by 5 ns", "restart from this rst7", "implicit-solvent MD", "GB implicit", "GBneck2", "igb=2", "OBC", "min → heat → density → prod", "production pmemd run", "pmemd.cuda", "antechamber", "parmchk2", "tleap", "AmberTools", "AmberTools25", "GAFF2", "AM1-BCC", "explicit-solvent ligand binding", "TIP3P+GAFF2 production". REMD trigger phrases — "T-REMD", "temperature REMD", "replica exchange", "parallel tempering", "exchange every", "temperature ladder", "geometric replica ladder", "exchange acceptance rate", "pmemd.cuda.MPI -rem 1", "demux REMD". Add-on trigger phrases (after-MD framing) — "MMPBSA", "MMGBSA", "endpoint binding free energy", "GB binding free energy", "PB binding free energy", "alanine scan", "per-residue decomposition", "score this trajectory", "cpptraj", "esander", "RMSD via cpptraj", "RMSF via cpptraj", "hbond analysis", "radgyr", "RDF of solvent around ligand", "per-frame energy decomposition". Routing — Amber-deep prompts (REMD, MMPBSA, cpptraj, ff19SB, OL21, esander, GB-implicit MD, alanine scan) reach this skill; ASE-shaped prompts (HOMO-LUMO, xTB, MACE, EMT, Gaussian DFT, slab building, Pt(111)) reach the sibling `ase-chemist` skill. The shared zone — GAFF2 + AM1-BCC + TIP3P + plain MD — is genuinely shared and either skill produces a correct answer.

The file declares its own license as MIT. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

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amber-chemist Skill (v1.0)

This skill is the Amber-native sibling to ase-chemist. It is MD-first: the v1.0 verb is normal (single-replica) MD with configurable stages, restart-and-extend, restraints, barostat options, explicit or implicit solvent, and a verbatim-mdin escape hatch. T-REMD is built on top of that core and ships in v1.0 too — currently the strongest differentiator vs ase-chemist's narrower v1.3 carve-out (which cannot do REMD). Analysis (cpptraj) and endpoint scoring (MMPBSA) are add-ons that consume the MD output, not co-equal verbs.

Always do this first

python scripts/check_env.py

The output ends with a [SUMMARY] line that names exactly which workflows your environment supports right now.

Environment-driven fallback strategy:

Parse the [SUMMARY] to determine available engines (pmemd.cuda, pmemd.cuda.MPI, pmemd, sander, etc.).
If the user requests REMD but only single-replica engines are available, always recommend single-replica MD as the fallback.
If the user requests MMPBSA scoring or cpptraj analysis but MMPBSA.py / cpptraj is not on PATH, report the gap clearly rather than fabricating a workaround.
Recommend the strongest path that the environment can run today; do not fabricate workarounds.

MD-core method selection

Task	Tool	Notes
One-shot pipeline (prep + min + heat + density + prod)	`scripts/amber_run.py`	Default mode `standard`. `--time 1ns` style. Use `--from-prmtop` to skip prep when the user has a CHARMM-GUI prmtop.
One-shot REMD pipeline	`scripts/amber_run.py --mode remd`	Chains prep + min + heat + density + REMD-prod. `--n-replicas`, `--t-low`, `--t-high`, `--exchange-every`. Requires `.MPI` engine.
One-shot implicit-solvent MD	`scripts/amber_run.py --mode implicit`	Skips solvateBox; skips density (no PBC). `--implicit-gb gb2`.
GAFF2 prep alone (small organic)	`scripts/amber_prep.py`	antechamber AM1-BCC → parmchk2 → tleap. `--water`, `--buffer`, `--box-shape oct`, `--salt-conc`.
Stage-level MD control	`scripts/amber_md.py --stage {min,heat,density,prod,custom}`	Per-stage flags: `--restraint-mask`, `--barostat monte_carlo`, `--implicit-solvent gb2`, `--mdin <file>` (escape hatch).
Restart from a previous stage	`scripts/amber_md.py --restart`	`irest=1, ntx=5`. Used for chaining heat→density→prod.
Extend an existing prod by N more ps	`scripts/amber_md.py --extend`	Auto-numbers `prod_2.{nc,rst7,mdout}`, `_3`, etc. Works on the same stage.
T-REMD (multi-replica enhanced sampling)	`scripts/amber_remd.py`	Auto temperature ladder, groupfile, exchange-rate report parsed from `rem.log`. Requires `.MPI` engine.

Deep dive: references/md_core.md for stage rendering, restart vs extend, restraints, barostat options, and implicit-solvent (GB) MD.

Barostat caveat: the default Berendsen barostat produces the wrong NPT distribution — use it for equilibration (the density stage) only. Switch production to --barostat monte_carlo for correct NPT ensemble averages. See references/md_core.md §Barostats.

Add-ons (consume MD output; not part of the MD core)

Framing: references/add_ons.md explains why add-ons consume MD output rather than acting as co-equal verbs, plus the extension-surface convention.

Add-on	Tool	Notes
Single-point energy on a snapshot	`scripts/amber_sp.py --mode snapshot`	`imin=5, maxcyc=0` via pmemd; returns decomposed energy. See `references/single_point.md` for the snapshot-vs-trajectory trade-off.
Per-frame energy decomposition over a trajectory	`scripts/amber_sp.py --mode trajectory`	cpptraj `esander` action; returns per-frame totals + components. See `references/single_point.md`.
RMSD / RMSF / RDF / hbond / radgyr	`scripts/amber_analyze.py`	cpptraj-driven; CSV + PNG per analysis. `--demux-remd --remd-dir <dir>` to demux a finished REMD into per-temperature trajectories.
Endpoint binding free energy (MMPBSA / MMGBSA)	`scripts/amber_score.py`	`--method gb

Force-field selection (v1.0)

Today: GAFF2 + AM1-BCC for small organics in TIP3P / OPC / SPCE / TIP4P-Ew water (or vacuum / implicit GB). That's the only path amber_prep.py runs.

--force-field {ff14SB, ff19SB, OL21} is pre-wired but raises NotImplementedError in v1.0. Biopolymer prep (proteins, nucleic acids, complexes) lands in v1.1. When the user asks for protein MD, say so honestly: this skill ships GAFF2-only today; ff19SB+OPC and OL21 are deferred. See references/extension_map.md for where each deferred feature would land.

Deep dive: references/force_fields.md for GAFF2/AM1-BCC details, supported water models (TIP3P / OPC / SPCE / TIP4P-Ew), and the deferred biopolymer set (ff19SB, OL21, LIPID17).

Engine selection

Workload	Auto-pick order	Override
Plain MD (`amber_md.py`)	`pmemd.cuda > pmemd > sander`	`--engine`
REMD (`amber_remd.py`)	`pmemd.cuda.MPI > pmemd.MPI > sander.MPI`	`--engine` (must be `.MPI`)

Auto-fail with a clear message if no engine of the right flavor is on PATH. AmberTools25 is fully open-source, including pmemd.cuda; if the user is on a fresh install and missing pmemd.cuda, point them at https://ambermd.org/GetAmber.php.

Verification & clarification

Don't ask what's already named — and frame what you do ask

The two failure modes to avoid: silently picking wrong physics (a wrong --net-charge shifts every AM1-BCC partial charge; a REMD ladder with 50 K gaps lands far below the 15-50% acceptance window; MMPBSA on an implicit-only prmtop is wrong physics), and re-asking the user something the prompt or input file already names.

When the answer is genuinely underdetermined, frame the question with the option you'd pick and the reason — e.g., "8 replicas geometric 300-400 K gives ~13–16 K gaps (widening with T), which should land inside the 15-50% acceptance window; keep that or hand-tune?" — beats a blank "what ladder?".

Ask the user to verify before recommending execution

After choosing parameters, restate them in a short block and ask the user to confirm before suggesting they run anything. What to surface depends on the verb:

Single-replica MD (amber_run.py --mode standard / amber_md.py):

Force field + water model (GAFF2 + TIP3P, etc.)
Net charge (silent-shift failure mode if wrong)
Engine (pmemd.cuda / pmemd / sander)
Buffer / box shape, salt conc if non-zero
Stage durations (heat ps, density ps, prod ns) and barostat
Restraints (mask + weight) if any
Output directory

T-REMD (amber_remd.py / amber_run.py --mode remd):

N replicas + T-low / T-high + ladder shape
Exchange-every (steps) and total time per replica
MPI engine + launcher (mpirun vs srun)
Implicit-solvent flag if relevant
Expected acceptance window — geometric gaps widen with T (~13–16 K for 8 replicas over 300–400 K is normal); flag only if a gap exceeds ~30 K or if N replicas is below 4. The script warns at >50 K.

Add-ons (amber_score.py, amber_analyze.py, amber_sp.py):

MMPBSA: method (gb / pb / both), igb model, ionic strength, frame range, MPI count
Analyze: which analyses (rmsd / rmsf / rdf / hbond / radgyr), masks, reference frame
SP: mode (snapshot / trajectory), frame slice (trajectory mode), engine

Keep it tight — a 4-6 line summary, not a paragraph. If the user has already approved the plan, don't re-ask.

Carve-out relationship with `ase-chemist`

ase-chemist's v1.3 carve-out does plain GAFF2 NPT MD only; amber-chemist is the deeper sibling (restart/extend, REMD, implicit solvent, cpptraj, MMPBSA). Shared-zone prompts (GAFF2 + AM1-BCC + TIP3P + plain MD) are correct from either. See references/carveout_relationship.md.

Looking up Amber semantics

For mdin keyword behavior, force-field options, and file formats, check references/mdin_keywords.md first (the ~50 most-asked keywords), then references/manual_lookup.md for Reference Manual sections and curated URLs. cpptraj and MMPBSA idioms live in references/cpptraj_idioms.md and references/mmpbsa_idioms.md.

Smell test — don't fabricate. If you are about to write "I think <keyword> defaults to ..." or "the standard value for <flag> is roughly ...", stop and check the manual first. Hallucinated Amber semantics is a high-cost, hard-to-detect failure mode — pmemd often runs with the wrong value and produces plausible-looking output that misleads downstream analysis.

Reporting results

When you finish a task, report:

The pipeline used (prep + stages, or REMD config, or scoring deck) and why it was chosen given system size, available engines, and what the user asked for.
Final numbers with units: trajectory length (ns), final temperature / density / volume parsed from the last mdout, REMD per-pair exchange acceptance rates (flag any outside [15%, 50%]), MMPBSA delta_total ± std-err if scoring.
Where outputs were written: prmtop / rst7 / .nc trajectory / mdout / exchange_rate.txt / <prefix>_summary.json.
Any caveats — e.g., "Berendsen for density only; prod ran with Monte Carlo", "REMD acceptance was 18% on the highest pair — borderline; consider one more replica", "MMPBSA GB-only — PB is ~2× slower but more defensible for publication".

Honest deferrals

When the user asks for something this skill does not ship — free energy (TI / FEP / MBAR), enhanced sampling beyond T-REMD (aMD, SMD, umbrella, metadynamics), Hamiltonian REMD, biopolymers (ff19SB / OL21), constant-pH, QM/MM, membrane/LIPID17, multi-GPU, PLUMED — point at references/extension_map.md for the concrete landing spot rather than fabricating a workflow. Do not pretend to support these. For features this skill DOES ship but where the user is hitting trouble, check references/failure_modes.md first (known failure modes + recovery recipes).