Major Version Update: 7.00.0

[drroe]

Changes in version 7.0 of CPPTRAJ. 2026

The major change in this version is the introduction of the ability of CPPTRAJ to fully build and parameterize systems in the same way that LEaP does.

New Commands

• build - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes prepareforleap and fixatomorder functionality. Can create macromolecular assemblies from PDBs with multiple models. Can solvate with a target # of solvent molecules.

• source - Read (limited) leaprc files.

• mutate - Mutate residues from one kind to another, keeping only common atoms.

• desc - DEBUG: describe a selection in the same manner as leap.

New functionality

• Read topology/coordinates with the 'readdata' command.

• More complete read of Amber library/prep files.

• Read CMAP energy term from Amber MDOUT file.

• The permutedihedrals command will now check rings.

• The graft command will now use CONNECT atom information if it is present.

• The energy command will now calculate CMAP energies (if CMAP parameters are present) and/or LJ 12-6-4 contributions to VDW energy (if lj1264 is specified).

• The sequence command now generates better geometries around bonds linking residues.

New Keywords

• Introduce ring intersection check to checkstructure action.

{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
               [ringacut <ringacut>]}]

Ring-bond intersections are detected when the ring center to bond center is less than , or less than and the angle between the bond vector and ring perpendicular vector is less than .

• Ignore extra points by default in the `checkstructure action.

[{checkxp | xpmask <xpmask>}]

If checkxp is specified, extra points will be included. By default, extra points will be ignored as determined by 'xpmask'; the default mask to select extra points is '&@\XP'

Add namemap <mapset> keywords for change atomname from <mask> to use an atom name map for determining new atom names.

Add gb to change command to change GB radii.

Add complete keyword to zmatrix command to get complete zmatrix instead of minimal zmatrix.

Add atombondorder keyword to mol2 output; sort bonds by first atom index (similar to how leap writes mol2 files).

Add lj1264 keyword to the energy command to enable LJ 12-6-4 energy calculation.

New file formats recognized

• Read Amber parameter (force field) files.

• Read Amber force field modification (frcmod) files.

• Read leaprc files (limited).

• Read atom/pdb residue name maps.

Misc Fixes

• Fix timing percentage of solute-solvent hydrogen bonds in hbond action.

• replicatecell action will correctly regenerate parameters as needed.

• Fix small memory leak when calculating modes.

• Ensure box information is properly updated if needed when using crdaction.

• Improve memory allocation in the Frame class to avoid frequent reallocation of memory.

• Improve handling of very large topology files.

• Better handling of very small boxes with pairlist code.

Not Yet Ready

• Introduce the byatom keyword to checkchirality action to check the chirality of any atoms in specified mask that are chiral centers.