amber

name	amber
description	Knowledge base from Amber 2026 Reference Manual and official tutorials. Code-first technical reference for AmberTools26/Amber26 — MD simulation, force fields, free energy, enhanced sampling, and trajectory analysis. Use when writing Amber commands, input files, or MD workflows.

Amber 2026 Technical Reference

Source: Amber 2026 Reference Manual (1112 pages, full distillation) + 83 official tutorials | Generated: 2026-07-11 | Chapters: 35

How to Use This Skill

• Without arguments — load this core reference
• With a program — ask about tleap, cpptraj, pmemd, antechamber, parmed, mdgx, MMPBSA.py, FEW, etc.
• With a workflow — ask about building systems, free energy, enhanced sampling, constant pH, membrane setup
• With chapter — ask for ch03 (LEaP), ch07 (MD engines), ch10 (CPPTRAJ), etc.
• Browse — ask "what chapters do you have?" to see the full index

When you ask about a topic not covered in Core Frameworks below, I will read the relevant chapter file before answering.

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Core Frameworks

The Amber MD Pipeline

PDB → pdb4amber → LEaP (prmtop+inpcrd) → sander/pmemd (mdin) → cpptraj (analysis)

Key files: prmtop (topology/parameters), inpcrd/rst7 (coordinates), mdin (namelist input), mdcrd/nc (trajectory)

Force Fields (Section 3)

Force Field	Use Case	leaprc source
FF19SB	Proteins	source leaprc.protein.ff19SB
FF14SB	Proteins (older)	source leaprc.protein.ff14SB
OL3/OL15/OL21	RNA	source leaprc.RNA.OL3
OL15/OL21	DNA	source leaprc.DNA.OL15
GAFF2	Small organic molecules	Used via antechamber
Lipid21	Lipids	source leaprc.lipid21
GLYCAM_06j	Carbohydrates	source leaprc.GLYCAM_06j
ff15ipq-m	Unnatural amino acids	source leaprc.ff15ipq

Water models: OPC (recommended for FF19SB), TIP3P, TIP4P-Ew, OPC3, SPC/E

MD Engines

Engine	Hardware	Key capability
sander	CPU	Full feature set, QM/MM, NMR
sander.MPI	CPU multi-node	Parallel sander
pmemd	CPU	Optimized, subset of sander
pmemd.cuda	GPU	High performance, recommended
pmemd.cuda.MPI	Multi-GPU	Multi-node GPU

Run command: pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r rst7 -x mdcrd -v mdvel -e mden -inf mdinfo -ref refcrd

mdin Namelist Structure

&cntrl        ! General MD control
  imin=0,     ! 0=MD, 1=minimization
  ntx=1,      ! 1=restart from inpcrd, 5=restart from rst7
  nstlim=100, ! Number of MD steps
  dt=0.002,   ! Timestep in ps (2 fs)
  ntt=3,      ! 1=Berendsen, 2=Andersen, 3=Langevin
  temp0=300.0, ! Target temperature (K)
  ntp=1,      ! 0=no pressure scaling, 1=isotropic
  ntb=2,      ! 1=no PBC, 2=constant P
  ntc=2,      ! 1=no SHAKE, 2=SHAKE on H-bonds
  ntf=2,      ! 1=all bonds, 2=omit H-bond forces
  cut=8.0,    ! Nonbonded cutoff (Å)
  ioutfm=1,   ! 0=ASCII, 1=NetCDF trajectory
  ntwx=5000,  ! Trajectory write frequency
  ntpr=500,   ! Print to mdout frequency
  ntwr=5000,  ! Restart write frequency
/
&ewald        ! Ewald/PME settings
  skinnb=2.0, ! Skin width for pairlist
/

CPPTRAJ — Core Analysis Commands

cpptraj -p prmtop -i script.in

Data loading: parm, trajin (load topology/trajectory) Actions: rms, rmsd, rmsf, distance, angle, dihedral, hbond, clustering, pca, strip, autoimage, center Output: writedata, run, go

Atom mask syntax: :1-10@CA (residues 1-10, Cα atoms), @/H (strip hydrogens), :WAT (water), :Na+ (sodium ions)

Antechamber — Small Molecule Parameterization

antechamber -i lig.mol2 -fi mol2 -o lig.mol2 -fo mol2 -c bcc -s 2 -nc 0
parmchk2 -i lig.mol2 -f mol2 -o lig.frcmod -s 2

Charge methods: -c bcc (AM1-BCC), -c resp (RESP), -c gas (Gasteiger)

LEaP — System Building

tleap -f leaprc.protein.ff19SB
> source leaprc.water.opc
> mol = loadpdb protein.pdb
> solvateoct mol OPCBOX 10.0
> addions2 mol Na+ 0
> addions2 mol Cl- 0
> saveamberparm mol prmtop inpcrd
> quit

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Chapter Index

Core MD Workflow (ch01–ch09)

#	Title	Key Programs
ch01	Installation & Quick Start	configure, cmake, conda, AMBERHOME
ch02	Force Fields & Molecular Mechanics	LEaP, leaprc, frcmod, ff19SB, ff14SB, OL3/15/21, Lipid21, GAFF2, OPC
ch03	LEaP: System Building	tleap, xleap, solvateoct, addions2, loadpdb, saveamberparm
ch04	PDB Preparation	pdb4amber, reduce
ch05	Antechamber & GAFF	antechamber, parmchk2, sqm, bcc, resp
ch06	parmed: Topology Manipulation	parmed, HMR, frcmod
ch07	sander: Complete Namelist Reference	sander, sander.MPI, full &cntrl + &ewald + &wt
ch08	Minimization, Heating & Relaxation	sander, pmemd, restraints, ntr, belly
ch09	pmemd & Production MD	pmemd, pmemd.cuda, pmemd.cuda.MPI, GPU, HIP, NFE, NEB

Trajectory Analysis (ch10)

| ch10 | CPPTRAJ: Trajectory Analysis | cpptraj, RMSD, PCA, clustering, tICA, MSM |

Free Energies (ch11–ch13, ch28, ch35)

#	Title	Key Programs
ch11	TI: Thermodynamic Integration	sander, pmemd, softcore, ACES
ch12	MM-PBSA & MMPBSA.py	MMPBSA.py, MM-GBSA, GB, PB
ch13	Umbrella Sampling & NFE	umbrella, WHAM, NFE toolkit, SMD, ABMD
ch28	BAR/PBSA Post-processing	bar_pbsa.py, edgembar, decharging
ch35	Free Energies: Complete Methodology	TI theory, softcore, GaMD-TI, quadrature

Enhanced Sampling & Equilibria (ch14–ch15)

| ch14 | Enhanced Sampling | REMD, GaMD, aMD, targeted MD, NEB, LMOD, WESTPA | | ch15 | Constant pH & Redox Potential | cphmd, cein, C(pH)MD, Marcus ET |

Force Field Development (ch16–ch17, ch24)

| ch16 | Force Field Development | mdgx, py_resp.py, RESP, IPolQ | | ch17 | Metal Ion Modeling | MCPB.py, pyMSMT, 12-6-4 LJ | | ch24 | paramfit: Parameter Fitting | paramfit, force constants |

System Types (ch18–ch20, ch25–ch27, ch34)

| ch18 | Membrane Systems | PACKMOL-Memgen, Lipid21, LiPi21 | | ch19 | QM/MM Overview | sander.MPI, QM/MM, QUICK | | ch20 | Implicit Solvent Overview | igb, pbsa, 3D-RISM, GBNSR6 | | ch25 | ProPrep: Protein Preparation | propred, interface modes | | ch26 | LES: Locally-Enhanced Sampling | les, multiple copy simulation | | ch27 | NAB: Nucleic Acid Builder | nab, nabc, nab2c, sff, molecule building | | ch34 | QM/MM: Detailed Namelist Reference | &qmmm, DFTB3, GFN2-xTB, QUICK, link atoms |

Advanced Tools (ch21–ch22)

| ch21 | Advanced Tools | FEW, GIST, APR, EMIL, MoFT | | ch22 | NMR, CryoEM, SAXS Refinement | sander, cpptraj |

Standalone Programs (ch23, ch29–ch33)

| ch23 | sqm: Semi-empirical QM | sqm, PM3, AM1, MNDO, DFTB, DFTB3, PM6, PM7, GFN2-xTB | | ch29 | RISM: Detailed Reference | rism1d, rism3d, 3D-RISM, rism3d.snglpnt, XRISM, DRISM | | ch30 | Torch PBSA | LibTorch, GPU-PB | | ch31 | GBNSR6: GB with R6 | gbnsr6, GB equations, R6 integration | | ch32 | External Library Interface | sander API, external energy/forces | | ch33 | PBSA: Detailed Reference | pbsa, PB solver, grid, nonpolar, membrane, GPU-PBSA |

Topic Index

• addions2 → ch03
• antechamber → ch05
• APR (Attach-Pull-Release) → ch21
• atom masks → ch10
• BAR → ch28
• bar_pbsa.py → ch28
• BCC charges → ch05
• CHARMM-GUI → ch03
• constant pH → ch15
• constant redox potential → ch15
• CPPTRAJ → ch10
• crystal simulation → ch03
• cutoff → ch07
• DFTB/DFTB3 → ch23
• DNA → ch02, ch03, ch27
• dvdl → ch35
• EMIL → ch21
• Enhanced sampling → ch14
• external library → ch32
• FEW (Free Energy Workflow) → ch21
• FF14SB → ch02
• FF19SB → ch02
• force field → ch02
• frcmod → ch02, ch16
• GAFF/GAFF2 → ch05
• GaMD → ch14
• GB (Generalized Born) → ch20
• GBNSR6 → ch31
• GFN2-xTB → ch23, ch34
• GIST → ch21
• GPU → ch09
• HMR (Hydrogen Mass Repartitioning) → ch06
• igb → ch20
• implicit solvent → ch20
• LEaP → ch03
• LES → ch26
• lipid → ch18
• LMOD → ch14
• MCPB.py → ch17
• mdgx → ch16
• mdin → ch07
• membrane → ch18
• minimization → ch08
• MM-PBSA → ch12
• MoFT → ch21
• NAB → ch27
• nabc → ch27
• namelist → ch07
• NEB → ch14
• NetCDF → ch07, ch10
• NFE → ch13
• NMR → ch22
• OPC water → ch02
• PACKMOL-Memgen → ch18
• paramfit → ch24
• parmchk2 → ch05
• parmed → ch06
• PBSA → ch33
• PCA → ch10
• pdb4amber → ch04
• pmemd → ch09
• pmemd.cuda → ch09
• pmemd.cuda.MPI → ch09
• prmtop → ch03, ch06
• ProPrep → ch25
• py_resp.py → ch16
• pyMSMT → ch17
• QM/MM → ch19, ch34
• QUICK → ch19
• REMD → ch14
• RESP → ch05, ch16
• restraints → ch08
• RISM → ch29
• RMSD → ch10
• RNA → ch02, ch03, ch27
• sander → ch07
• SHAKE → ch07
• softcore → ch11, ch35
• solvateoct → ch03
• sqm → ch23
• steered MD → ch14
• Thermodynamic Integration → ch11, ch35
• tleap → ch03
• Torch PBSA → ch30
• umbrella sampling → ch13
• WESTPA → ch14
• WHAM → ch13
• XMIN → ch07

Tutorial Traceability

When answering a query:

1. Find the relevant chapter(s) in the index below
2. Cross-reference with TUTORIALS.md to find the original worked examples in manuals/tutorials/
3. Load the tutorial file(s) for concrete, step-by-step code examples to accompany the chapter reference

Example query flow: "metal ion simulation" → ch17 (Metal Ion Modeling) → TUTORIALS.md shows: 02-4_Metal Ion Modeling Tutorial.md + 01-12-1_Protein-Metal.md → load those tutorials for worked examples.

Supporting Files

• glossary.md — all key terms with definitions
• patterns.md — common workflows and design patterns
• cheatsheet.md — quick reference tables and decision guides
• TUTORIALS.md — chapter → tutorial cross-reference for source traceability

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Scope & Limits

This skill covers AmberTools26 and Amber26 content from the official Reference Manual and tutorials. It is code-first: every concept is grounded in working commands, input file snippets, and exact flag syntax. For theory and background, consult the Amber Reference Manual PDF directly. For project-specific implementation, combine with the user's actual system setup.