I am applying to a PhD programme and am planning to take recommendation letter from an Emeritus professor who has known me for past 5 years. However, the professor does not use college id any longer and has asked me to provide his gmail account for electronic submission of recommendation letter. Will using such id harm my prospects as a PhD candidate? Should I use some active professor instead?
No, the form of the email address won't matter. You want letters from those who can best support your candidacy, so don't bother with others. If they are the best choice to support you, then get the letter from them. Someone with emeritus status has had a long career and is probably well known.
Of course, a former professor should identify them self as such in the letter, naming the institution.
I doubt that electronic systems will block you, as not all letters come from academics in any case.
Some of us still maintain university hosted web sites and are listed among emeritus faculty.