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pytraj and cpptraj offer limited Topology editing. For more features and power, please do visit ParmEd

Load topology

From iterload

import pytraj as pt
traj = pt.iterload('', '2KOC.parm7')
top =

From load_topology

top = pt.load_topology('2KOC.parm7')

Supported file formats


cpptraj/pytraj (and parmed) recognizes file by its content, not by extention. So it’s ‘legal’ to use


(table was adapted from Amber15 manual)

Format Extension Notes
Amber parm7 Write/Read
PDB pdb Read Only
Mol2 mol2 Read Only
CIF cif Read Only
Charmm PSF psf Limited PSF Write
SDF sdf Read Only
Tinker ARC arc Read Only

Topology editing

  • slicing a Topology

    top = pt.load_topology('2koc.pdb')
  • save to different format

    top = pt.load_topology('2koc.parm7')'test.mol2')