fixatomorder

Fix atom ordering so that all atoms in molecules are sequential.

fixatomorder [outprefix <name>]

CPPTRAJ (and most of Amber) expects that atom indices in molecules to increase monotonically. However, occasionally atom indices in molecules can become disordered. This command fixes atom ordering so that all atoms in molecules are sequential. The outprefix keyword will write out the re-ordered topology with name:
<name>.<original name>.