[gmx-users] TOP file question

[Peter Eastman]

I'm implementing a TOP file reader, and I have a question about an ambiguity in the format.  The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions).  In addition, the gen-pairs flag can indicate that pairs are generated automatically.  But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that.

Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones?

Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else?

What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically?  Which should I use?

Thanks.

Peter