Skill: ning-kun/amber-md (version 1.0.4)

--- 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 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 Å - 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 — create directories ```bash mkdir -p amber_1aki/{input,build,md,analysis,logs} cd amber_1aki ``` ### Step 2 — 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 — 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 — 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 — 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 — 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 — 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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