Let be your system a complex with a ligand named LIG.
Open a ptraj.in and add the following lines:
trajin rec.all.mdcrd
reference rec.crd
center ~:WAT,Na+,Cl-
image byres :WAT,Na+,Cl-
rms reference mass out rmsREC @CA
rms reference mass out rmsLIG :LIG nofit
atomicfluct out flucREC ~:WAT,Na+,Cl-,LIG byres
rms reference mass out rmsLIGfit :LIG
Now enter ptraj rec.top < ptraj.in
You should see three different files: rmsREC (RMSD of Cα atoms of the target), rmsLIG (RMSD of all atoms of the ligand), flucREC (RMSD fluctuations of the residues of the target)