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

Standard workflow summary

Recommended directory layout

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

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:

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

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:

Stage 1 minimization
 &cntrl
  imin=1,
  maxcyc=5000,
  ncyc=2500,
  ntb=1,
  ntr=0,
  cut=10.0,
  ntpr=500,
 /

Run:

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:

Stage 2 minimization
 &cntrl
  imin=1,
  maxcyc=10000,
  ncyc=5000,
  ntb=1,
  ntr=0,
  cut=10.0,
  ntpr=1000,
 /

Run:

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:

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:

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:

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:

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:

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:

pmemd.cuda -O \
  -i prod.in \
  -o prod.out \
  -p ../build/prmtop \
  -c equil.rst7 \
  -r prod.rst7 \
  -x prod.nc

Useful duration reference

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:

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:

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

mkdir -p amber_1aki/{input,build,md,analysis,logs}
cd amber_1aki

Step 2 — download and preprocess structure

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

cat > build/tleap.in \x3C\x3C '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:

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

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

cat > analysis/analyze.cpptraj \x3C\x3C '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

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

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.