All the programs and datafiles should reside in the same directory. This should be logically defined in the command file AMPS.COM. Simply change the assign statements to indicate the directory that you have put AMPS in.
Executing the file AMPS.COM will set up the necessary logical names.
Thereafter, all the above examples as described should work. However, you will have to modify the command files as supplied to agree with the examples shown above.
Not all the programs work under VMS. MULTALIGN and ORDER should be OK. I've no plans to port the other programs to VMS.