"One point that is not made clearly in the manual is how to specify the connectivity between residues. This mechanism is protein-specific, and relies on the existence in each residue of atoms with the same names, i.e. the protein backbone atoms. The
[ bonds ]section in the example in section 5.6.1 of the manual defines a bond between
N. This refers to the
Catom in the previous residue. Similarly, one might use a
+Nprefix to refer to the
Natom in the following residue."
This meant I never defined how the residues were connected together in my .rtp file. This explains why I got a bunch of short bond warnings and my topology file never had pairs, angles or dihedrals.
I've changed the [bonds] section of the .rtp from the cnt carbons to:
C C 0 0
C C 0 0
[ bonds ]
C +C 0.14210 478900
However I can't be certain that adding a +C to the second C in all the bonds makes sense for all of them. I guess I need to know how you put together a large protein and then figure out how you assemble a carbon nanotube using the same basic steps...