1. I’ve put up Glenn’s tutorial on loop modeling in the hopes that it might make things a little clearer: Loop Modeling
2. pNNMAKE does not accept a zone file, the zone file is for make_fragments.pl
3. We are in the process of debugging the C++ version of pNNMAKE. I’m not sure when it will be available (but at this point, we are just trying to make sure it behaves like pNNMAKE).
> There is a section on Comparative Modeling Comparative Modeling that I just can’t get to work. Does pNNMAKE actually accept a zone file? There is no mention in the nnmake code of zone file or “loops_all”. This is an option in make_fragments.pl, however. Is there a newer version of pNNMAKE available?