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Amber Molecular Dynamics Simulation

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Official-style Amber24 molecular dynamics workflow guide for proteins. Includes a standard end-to-end Amber MD procedure, command templates, input-file templ... Skill: Amber Molecular Dynamics Simulation Owner: ning-kun Summary: Official-style Amber24 molecular dynamics workflow guide for proteins. Includes a standard end-to-end Amber MD procedure, command templates, input-file templ... Tags: amber:1.0.4, latest:1.0.4, md:1.0.4, molecular-dynamics:1.0.4, simulation:1.0.4 Version history: v1.0.4 | 2026-04-25T10:24:54.717Z | user v1.0.4: upgraded public documentation into an o

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About

What it does, and when to use it.

Capability contract not published. No trust telemetry is available yet. 994 downloads reported by the source. Last updated 10/11/2026.

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Install and run

Setup complexity: low.

clawhub skill install s1793t9ymha9akcjnvdf34p37584zr5m:amber-md
  1. Setup complexity is LOW. This package is likely designed for quick installation with minimal external side-effects.
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Contract: missing

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Run-check

$0.02 USD

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Documentation

CLAWHUB

50,959 characters of source documentation, loaded on request.

Extracted files

5 files captured from the source.

SKILL.md

---
name: amber-md
description: |
  Official-style Amber24 molecular dynamics workflow guide for proteins. Includes a standard end-to-end Amber MD procedure, command templates, input-file templates, and a complete manual worked example from PDB download through RMSD/RMSF analysis. This is a documentation-oriented scientific skill for reproducible research workflows in Amber.
metadata:
  {
    "openclaw":
      {
        "emoji": "🧬",
        "examples":
          [
            "how do I run Amber MD on a protein?",
            "show me a standard Amber workflow with commands",
            "give me a complete manual example for Amber RMSD and RMSF analysis"
          ]
      }
  }
---

# Amber Molecular Dynamics Simulation

## Overview

This skill is designed as an **official-style documentation page** for running a standard protein molecular dynamics workflow with **Amber24 / AmberTools24**.

It is intentionally **documentation-first**:
- it explains the canonical workflow,
- provides reusable command templates,
- provides input-file templates,
- and gives a full manual example that users can reproduce step by step.

It does **not** bundle executable automation scripts inside the public ClawHub package.

---

## What this skill helps you do

Use this skill when you need to:

1. prepare a protein structure from the PDB database,
2. build a solvated Amber system,
3. run minimization, heating, equilibration, and production MD,
4. analyze the trajectory with `cpptraj`,
5. understand what outputs to expect and how to judge simulation quality.

---

## Recommended Amber tools

| Tool | Main purpose |
|---|---|
| `pdb4amber` | preprocess PDB structures for Amber |
| `tleap` | build topology and coordinates |
| `pmemd.cuda` | GPU production MD |
| `pmemd` | CPU fallback |
| `cpptraj` | trajectory analysis |
| `antechamber` | ligand parameterization when needed |
| `parmchk2` | missing force-field terms for ligands |

---

## Standard workflow summary

| Stage | Goal | Main output |
|---|---|---|
| 1. Structure preparation | clean and standardize input structure | processed PDB |
| 2. System building | add force field, solvent, ions | `prmtop`, `inpcrd` |
| 3. Minimization | remove bad contacts | minimized restart file |
| 4. NVT heating | raise temperature to target value | heated restart + trajectory |
| 5. NPT equilibration | stabilize density and pressure | equilibrated restart + trajectory |
| 6. Production MD | generate scientific trajectory | production trajectory |
| 7. Analysis | compute RMSD/RMSF and related metrics | data tables and plots |

---

## Recommended directory layout

```text
project/
├── input/
│   └── protein.pdb
├── build/
├── md/
├── analysis/
└── logs/
```

A simpler flat directory also works, but a structured layout improves reproducibility.

---

## 1. Structure preparation

### Recommended rules

- If the PDB entry contains multiple NMR models, start with **Model 1**.
- Remove unsupported ligands if you do not have parameter

_meta.json

{
  "ownerId": "kn76km32bz2x4rjp91mb223h5982sd5q",
  "slug": "amber-md",
  "version": "1.0.4",
  "publishedAt": 1777112694717
}

references/amber_parameter_guide.md

# Amber MD Parameter Guide

## Core controls
- `nstlim`: number of MD steps
- `dt`: timestep in ps
- `temp0`: target temperature
- `ntb`: box / boundary mode
- `ntp`: pressure coupling
- `cut`: nonbonded cutoff
- `ntwx`: trajectory write interval
- `ntpr`: energy print interval

## Common durations
- 1 ns: `nstlim=500000` with `dt=0.002`
- 10 ns: `nstlim=5000000`
- 100 ns: `nstlim=50000000`

## Typical production settings
- Temperature: 300 K
- Pressure: 1 atm
- Timestep: 2 fs
- Ensemble: NPT

references/cpptraj_analysis_guide.md

# cpptraj Analysis Guide

## Recommended analysis order
1. Load topology
2. Load trajectory
3. Strip water and ions if appropriate
4. Apply `autoimage`
5. Compute RMSD
6. Compute RMSF

## Typical outputs
- RMSD time series
- RMSF per residue
- Radius of gyration
- Hydrogen-bond summaries

## Common pitfalls
- Using all atoms including solvent for RMSD
- Inconsistent masks between reference and trajectory
- Forgetting periodic imaging correction

skill-card.md

## Description:

Official-style Amber24 molecular dynamics workflow guide for proteins, including a standard end-to-end procedure, command templates, input-file templates, and a manual worked example from PDB download through RMSD/RMSF analysis.

This skill is ready for commercial/non-commercial use.

## Publisher:

[ning-kun](https://clawhub.ai/user/ning-kun)

### License/Terms of Use:

MIT-0

## Use Case:

Scientists, educators, and technical users use this skill to plan and manually run reproducible Amber protein molecular dynamics workflows, from structure preparation through trajectory analysis. It provides workflow guidance, command templates, and quality checks rather than executable automation.

### Deployment Geography for Use:

Global

## Known Risks and Mitigations:

Risk: Amber simulations can consume substantial compute or GPU time and create local output files.

Mitigation: Review commands before execution, validate with the documented 1 ns workflow first, and run in an appropriate project directory with expected storage and compute capacity.

Risk: Scientific results can be misleading if input structures, ligands, atom masks, or imaging choices are inappropriate.

Mitigation: Follow the documented quality checks, remove or parameterize unsupported ligands, use consistent atom masks, and apply trajectory imaging correction before interpreting RMSD or RMSF.

## Reference(s):

- [Amber Parameter Guide](references/amber_parameter_guide.md)
- [cpptraj Analysis Guide](references/cpptraj_analysis_guide.md)
- [1AKI PDB Download](https://files.rcsb.org/download/1AKI.pdb)

## Skill Output:

**Output Type(s):** [text, markdown, shell commands, configuration, guidance]

**Output Format:** [Markdown guidance with inline bash commands and Amber input-file templates]

**Output Parameters:** [1D]

**Other Properties Related to Output:** [Documentation-only output; users review and run commands manually in their Amber environment.]

## Skill Version(s):

1.0.4 (source: server release evidence and artifact metadata)

## Ethical Considerations:

Users should evaluate whether this skill is appropriate for their environment, review any generated or modified files before relying on them, and apply their organization's safety, security, and compliance requirements before deployment.

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