The form of your data in your original file, Error file.nb, is of the form
{
{{_,_,_}...}
}
whereas the form of the data in your recent example file reply.nb is of this form:
{{_,_,_}...}
When I take the first part of the data in your original file so that the form that is being supplied to the first argument of the NonlinearModelFit function is like the one in your second notebook, {{,,_}...}, then I no longer get the "non-negative numbers" message (but I do get a variety of InterpolatingFunction messages as well as some warning from NDSolve pertaining to some difficulty in the convergence of the numerical methods used by NDSolve).
