A month ago I received the referees' comments on a paper: two are positive, but the other one is negative. In particular, there is a very "negative" comment in this report:
All of the physical effects considered here have been considered before, and model equation is an obvious and not especially interesting generalization of similar equations elsewhere in the literature.
How can I give an appropriate reply to this comment?
Well if you disagree with the comment, then you offer a sound, well-reasoned counterargument that addresses the concerns. If your equation is interesting, then why? If it is not obvious, then why? Do these alleged equations/models only look similar, but in fact there's a deeper and possibly subtle distinction? If so, point it out. Non-combatively.
These are the sorts of things that often get addressed in the introduction. Possibly the remark is ultimately a reflection on your paper having a weak introduction that fails to address the "what's new here and why should I care?" questions with sufficient flair, clarity, and authority. More than one legitimately good paper (to whatever extent such a benchmark exists objectively) has been rejected because the authors failed to do an adequate job of "selling" and explaining the paper in the abstract and introduction.
Of course, there's also the possibility that the remark is spot-on. One reason journals tend to use multiple referees is because there's no guarantee that any one expert has authoritative and unbiased knowledge on whatever bits of arcana your paper is using. Nor is there a guarantee for two, or three, or whatever, but the odds are better that if something is "wrong" from the standards of the journal then it will be found.
A literature review is the way to delve into this possibility. "Elsewhere in the literature" would suggest to me that the reviewer believes you have intentionally or accidentally excluded some important pieces of the literature, and this can only be resolved by looking further into the literature (and possibly asking colleagues if they know of anything that might seem relevant).
If ultimately you end up agreeing with the comments, in part or in whole, that can be a tough pill to swallow, but reality is what it is. You can still try to rewrite portions of the paper to properly address preceding similar work and argue why yours is in some sense novel, interesting, and/or useful. And then you either hope this placates the negative reviewer sufficiently to earn acceptance, or you submit it to some other journal after a rejection. "Minor generalizations" are sometimes simply not up to snuff for certain journal standards, while it is well within that of others.