Tom,

I believe this is the information you need. I found the following in "Report of the Adjutant General of the State of Indiana," Vol. II:

1st Lieutenant John Murphy, Company D, 40th Indiana Volunteer Infantry. Place of Residence: Battle Ground (Tippecanoe County), Indiana. Date of Commission: 30 December 1861. Date of Muster: 30 December 1861. Resigned commission for unspecified reasons (possibly due to medical reasons): 26 November 1862.

Let me know if you need any further help.

Regards,

Mark Jaeger