Official-style Amber24 molecular dynamics workflow guide for proteins. Includes a standard end-to-end Amber MD procedure, command templates, input-file templ...
---
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": "๐งฌ",
"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/
โโโ input/
โ โโโ protein.pdb
โโโ build/
โโโ md/
โโโ analysis/
โโโ 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 parameters for them.
- Keep the protein-only workflow as the default baseline.
- Use `pdb4amber` to standardize residue names and protonation-related formatting.
### Command template
```bash
mkdir -p input build md analysis logs
cd project
# download from RCSB
wget -O input/1AKI.pdb https://files.rcsb.org/download/1AKI.pdb
# preprocess
pdb4amber -i input/1AKI.pdb -o input/1AKI_amber.pdb --reduce > logs/pdb4amber.log 2>&1
```
### Notes
- If preprocessing fails because of nonstandard residues, inspect the structure first.
- For protein-only tutorials, removing unsupported ligands is often the most robust starting point.
---
## 2. System building with tleap
### Recommended setup
- Protein force field: `ff19SB`
- Water model: `OPC`
- Box type: truncated octahedron
- Padding: ~15 ร
- Neutralization: `Na+` / `Cl-`
### `tleap` input template
Save as `build/tleap.in`:
```bash
source leaprc.protein.ff19SB
source leaprc.water.opc
mol = loadPDB ../input/1AKI_amber.pdb
desc mol
addions mol Cl- 0
addions mol Na+ 0
solvateOct mol OPCBOX 15.0
addions2 mol Na+ 0
addions2 mol Cl- 0
saveAmberParm mol prmtop inpcrd
savePDB mol solvated.pdb
quit
```
### Run command
```bash
cd build
tleap -f tleap.in > ../logs/tleap.log 2>&1
```
### Expected outputs
- `build/prmtop`
- `build/inpcrd`
- `build/solvated.pdb`
---
## 3. Energy minimization
A common two-stage minimization is sufficient for many small-to-medium protein systems.
### Stage 1 minimization template
Save as `md/min1.in`:
```bash
Stage 1 minimization
&cntrl
imin=1,
maxcyc=5000,
ncyc=2500,
ntb=1,
ntr=0,
cut=10.0,
ntpr=500,
/
```
Run:
```bash
cd md
pmemd.cuda -O \
-i min1.in \
-o min1.out \
-p ../build/prmtop \
-c ../build/inpcrd \
-r min1.rst7
```
### Stage 2 minimization template
Save as `md/min2.in`:
```bash
Stage 2 minimization
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntb=1,
ntr=0,
cut=10.0,
ntpr=1000,
/
```
Run:
```bash
pmemd.cuda -O \
-i min2.in \
-o min2.out \
-p ../build/prmtop \
-c min1.rst7 \
-r min2.rst7
```
---
## 4. NVT heating
### Heating template
Save as `md/heat.in`:
```bash
NVT heating
&cntrl
imin=0,
irest=0,
ntx=1,
nstlim=50000,
dt=0.002,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ntb=1,
cut=10.0,
ntpr=5000,
ntwx=5000,
/
```
Run:
```bash
pmemd.cuda -O \
-i heat.in \
-o heat.out \
-p ../build/prmtop \
-c min2.rst7 \
-r heat.rst7 \
-x heat.nc
```
---
## 5. NPT equilibration
### Equilibration template
Save as `md/equil.in`:
```bash
NPT equilibration
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=100000,
dt=0.002,
ntf=2,
ntc=2,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ntb=2,
ntp=1,
pres0=1.0,
cut=10.0,
ntpr=10000,
ntwx=10000,
/
```
Run:
```bash
pmemd.cuda -O \
-i equil.in \
-o equil.out \
-p ../build/prmtop \
-c heat.rst7 \
-r equil.rst7 \
-x equil.nc
```
---
## 6. Production MD
### 1 ns production template
Save as `md/prod.in`:
```bash
Production MD
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=500000,
dt=0.002,
ntf=2,
ntc=2,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ntb=2,
ntp=1,
pres0=1.0,
cut=10.0,
iwrap=1,
ntpr=25000,
ntwx=12500,
/
```
Run:
```bash
pmemd.cuda -O \
-i prod.in \
-o prod.out \
-p ../build/prmtop \
-c equil.rst7 \
-r prod.rst7 \
-x prod.nc
```
### Useful duration reference
| Target time | `nstlim` with `dt=0.002 ps` |
|---|---|
| 1 ns | 500000 |
| 10 ns | 5000000 |
| 100 ns | 50000000 |
---
## 7. Trajectory analysis with cpptraj
### Recommended analysis procedure
Before RMSD/RMSF:
- strip solvent and ions if you want protein-only metrics,
- apply `autoimage`,
- use a consistent atom mask.
### `cpptraj` template
Save as `analysis/analyze.cpptraj`:
```bash
parm ../build/prmtop
trajin ../md/prod.nc 1 last 1
strip :WAT
strip :Na+
strip :Cl-
autoimage
rms out rmsd_ca.dat
atomicfluct out rmsf_ca.dat
run
```
Run:
```bash
cd analysis
cpptraj -i analyze.cpptraj > ../logs/cpptraj.log 2>&1
```
### Typical outputs
- `analysis/rmsd_ca.dat`
- `analysis/rmsf_ca.dat`
- `logs/cpptraj.log`
---
## Full manual example: protein-only 1 ns Amber MD
This example shows a minimal, reproducible manual workflow using **1AKI**.
### Step 1 โ create directories
```bash
mkdir -p amber_1aki/{input,build,md,analysis,logs}
cd amber_1aki
```
### Step 2 โ download and preprocess structure
```bash
wget -O input/1AKI.pdb https://files.rcsb.org/download/1AKI.pdb
pdb4amber -i input/1AKI.pdb -o input/1AKI_amber.pdb --reduce > logs/pdb4amber.log 2>&1
```
### Step 3 โ create `build/tleap.in`
```bash
cat > build/tleap.in << 'EOF'
source leaprc.protein.ff19SB
source leaprc.water.opc
mol = loadPDB ../input/1AKI_amber.pdb
addions mol Cl- 0
addions mol Na+ 0
solvateOct mol OPCBOX 15.0
addions2 mol Na+ 0
addions2 mol Cl- 0
saveAmberParm mol prmtop inpcrd
savePDB mol solvated.pdb
quit
EOF
```
Run:
```bash
cd build
tleap -f tleap.in > ../logs/tleap.log 2>&1
cd ..
```
### Step 4 โ create minimization, heating, equilibration, and production input files
Use the exact templates from the sections above:
- `md/min1.in`
- `md/min2.in`
- `md/heat.in`
- `md/equil.in`
- `md/prod.in`
### Step 5 โ run MD
```bash
cd md
pmemd.cuda -O -i min1.in -o min1.out -p ../build/prmtop -c ../build/inpcrd -r min1.rst7
pmemd.cuda -O -i min2.in -o min2.out -p ../build/prmtop -c min1.rst7 -r min2.rst7
pmemd.cuda -O -i heat.in -o heat.out -p ../build/prmtop -c min2.rst7 -r heat.rst7 -x heat.nc
pmemd.cuda -O -i equil.in -o equil.out -p ../build/prmtop -c heat.rst7 -r equil.rst7 -x equil.nc
pmemd.cuda -O -i prod.in -o prod.out -p ../build/prmtop -c equil.rst7 -r prod.rst7 -x prod.nc
cd ..
```
### Step 6 โ analyze trajectory
```bash
cat > analysis/analyze.cpptraj << 'EOF'
parm ../build/prmtop
trajin ../md/prod.nc 1 last 1
strip :WAT
strip :Na+
strip :Cl-
autoimage
rms out rmsd_ca.dat
atomicfluct out rmsf_ca.dat
run
EOF
cd analysis
cpptraj -i analyze.cpptraj > ../logs/cpptraj.log 2>&1
cd ..
```
### Step 7 โ inspect results
```bash
ls -lh md/prod.nc analysis/rmsd_ca.dat analysis/rmsf_ca.dat
```
Expected scientific interpretation:
- RMSD reaches a stable plateau after equilibration,
- RMSF is higher at loops and termini,
- temperature remains close to 300 K,
- pressure fluctuates around 1 atm during NPT stages.
---
## Common quality checks
| Check | What to look for |
|---|---|
| Minimization | energy decreases and no severe bad contacts remain |
| Heating | temperature ramps smoothly toward 300 K |
| Equilibration | density/pressure behavior stabilizes |
| Production RMSD | plateau rather than monotonic drift |
| RMSF | flexible regions match structural expectation |
---
## Common pitfalls
1. **Using all atoms including water for RMSD**
- this often produces meaningless large RMSD values.
2. **Ignoring ligands with missing parameters**
- remove them or parameterize them first.
3. **Using inconsistent atom masks**
- reference and trajectory selections must match.
4. **Skipping `autoimage`**
- periodic boundary effects can distort analysis.
5. **Starting with too large a target simulation**
- validate the workflow with 1 ns before 100 ns.
---
## Ligands and nonstandard residues
If your structure contains:
- a ligand,
- a cofactor,
- a metal center,
- a nucleotide analog,
- or another nonstandard residue,
then you may need:
- `antechamber`,
- `parmchk2`,
- additional `tleap` libraries,
- or specialized workflows such as `MCPB.py`.
For a first-pass reproducible workflow, a **protein-only simulation** is often the most robust baseline.
---
## References included in this skill
- `references/amber_parameter_guide.md`
- `references/cpptraj_analysis_guide.md`
---
## Intended use
This public ClawHub version is intended for:
- scientific education,
- workflow standardization,
- project planning,
- manual reproducible Amber execution.
It is a **public documentation edition** rather than a bundled executable automation package.
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