By hand it is, then. But I'm still not clear on where I can find out how to create an IC table by hand, even if it only lists dihedral terms... e.g.,
How does one determine what dihedrals (proper and improper) need to be listed in the IC table of the rtf?
This is what I used the IC gene before, not the values (which indeed had to be edited as predicted, which I did). I had read what you quoted from intcor.doc and the subsequent numbered list.
Now, looking at the rtf for the adenine in AMP from the CGENFF rtf I see that improper dihedrals are defined in the IC table with central atoms C2, C4, C6, N6, C8, and N9. This is all of the impropers that I can see in this section of the molecule, except for the one with C5 as the central atom
. Why is there no dihedral term with C5 as the central atom? If there were
such a term listed, I feel like I'd have a pretty good sense of which ones I'd need to define for my fragment (those with central atoms C2, C4, C5, C6, N6, N7, C8, C9). Also, the lines with C6 and N6 are exactly duplicated; I assume these duplicates are extras that have not been deleted.
Then, for the (proper) dihedrals I see that one dihedral term for 6 pairs of central atoms are defined once (one is duplicated exactly). I can see not needing to define multiple terms for each pair of central atoms, but why are there no dihedrals at all for X-C6-N1-X or X-N1-C2-X or X-C2-N3-X or X-C4-C5-X or X-N7-C8-X ? It seems that understanding this is crucial for creating an IC table by hand...
(Looking back at my stream file, I see at least one typo or nonsensical dihedral created by ic gene, not sure which but I'll assume typo by me...)
Thank you for all your help.