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 for write
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 Read Only
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.
change Change specified parts of a topology.
charge Print total charge for selected atoms.
comparetop Compare two topologies and report differences.
dihedralinfo, dihedrals, printdihedrals Print dihedral info for selected atoms.
hmassrepartition Perform hydrogen mass repartitioning.
improperinfo, impropers, printimpropers Print improper 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.
printub, ubinfo Print Urey-Bradley info for selected atoms.
resinfo Print residue info for selected atoms.
scaledihedralk Scale selected dihedral force constants.
solvent Change which molecules are considered solvent.
updateparameters Update/add parameters in/to a topology.