Command Reference
Ready
Ln 1, Col 1
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CPPTRAJ SCRIPT
Output Terminal
● IDLE
CpptrajAI — Molecular Dynamics Analysis Studio
Upload topology + trajectory files, write your script, click ▶ Run.
Use ⚙ in the header to set your Anthropic API key for the AI Agent.
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Project Files
Drop topology (.prmtop) &
trajectory (.nc, .dcd, .xtc) here
trajectory (.nc, .dcd, .xtc) here
Test Data
ready to use
Solvated protein · 30070 atoms · 9157 res · 10 frames · AMBER NetCDF
Mask Cheat Sheet
:1Residue 1
:1-100Residues 1–100
:ALAAll alanines
@CAAll Cα atoms
@CA,C,N,OBackbone atoms
!:WATExclude water
:1-50&@CACα of res 1–50
:LIG<:5.0Within 5 Å of LIG
@/CAll carbons