This is an old revision of the document!
ptraj.in and add the following lines:
ptraj rec.top < ptraj.in
But if you need some waters around your ligand or QMMM region? No problem! Forget 'strip' and add these lines to your ptraj.in:
solvent byres :WAT
closestwater 20 :464 first (WAT around residue 464 until 20 A of distance will be preserved)