Topology File Commands


These commands control the reading and writing of topology files. Cpptraj supports the following topology file

Format Keyword Extension Notes
Amber Topology amber .parm7 Only fully-supported format
PDB pdb .pdb Read Only
Mol2 mol2 .mol2 Read Only
CIF cif .cif Read Only
Charmm PSF psf .psf Limited Write
Gromacs Topology gromacs .top Limited Write
SDF sdf .sdf Read Only
Tinker ARC arc .arc Read Only

For most commands that require a topology one can be specified via two keywords:
parm [<name>] Select topology corresponding to given file name, tag, or name.
parmindex [<#>] Select topology by order in which it was loaded, starting from 0.

The following topology related commands are available:

Command Description
angleinfo, angles, printangles Print angle info for selected atoms
atominfo, atoms, printatoms Print details for selected atoms
bondinfo, bonds, printbonds Print bond info for selected atoms
charge Print total charge for selected atoms.
comparetop Compare two topologies and report differences.
dihedralinfo, dihedrals, printdihedrals Print dihedral info for selected atoms.
mass Print total mass for selected atoms.
molinfo Print molecule info for selected atoms.
parm Load a topology file.
parmbox Modify box info for a loaded topology
parminfo Print details for selected topology
parmstrip Remove selected atoms from topology.
parmwrite Write selected topology to file.
resinfo Print residue info for selected atoms.
scaledihedralk Scale selected dihedral force constants
solvent Change which molecules are considered solvent