Topology

try pytraj online:

Note

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('traj.nc', '2KOC.parm7')
top = traj.top

From load_topology

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

Supported file formats

Note

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

pt.load_topology(‘2koc.very_very_long_ext’)

(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')
    top['@CA']
    
  • save to different format

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