Open ptraj.in and add the following lines:
trajin rec.h.mdcrd
trajin rec.eq1.mdcrd
trajin rec.eq2.mdcrd
trajin rec.eq3.mdcrd
trajin rec.eq4.mdcrd
trajin rec.eq5.mdcrd
trajin rec.md1.mdcrd
trajin rec.md2.mdcrd
trajin rec.md3.mdcrd
trajin rec.md4.mdcrd
trajin rec.md5.mdcrd
trajin rec.md6.mdcrd
…
trajout rec.all.mdcrd
Now execute ptraj rec.top < ptraj.in