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')