Does anyone know if it is possible to use InterfaceAnalyzer only on a subset of atoms instead of the whole proteins?
Specifically, I've recently completed 4x 2 us simulations in GROMACS and would like to understand how different positions/polar/hydrogen bonding networks of an interface loop affect interaction energy between the two proteins.
If this cannot be done, I suppose an alternative approach would be to strip all non-relevant residues with awk and then run only the subsets through InterfaceAnalyzer
InterfaceAnalyzer was not written to work on subsets of atoms or residues. It would not be hard to do that in PyRosetta.
If you have a bunch of similar structures, just run them as-is through InterfaceAnalyzer: the constant regions will wash out in the analysis, because you're looking at deltas/differences not absolutes.
Stripping irrelevant residues may lead to strange behavior, as the scorefunction is written for intact protein. If you feed it bunches of isolated residues, backbone-dependent terms (like the rotamer energy) will give wrong results because phi/psi aren't defined. Also, the hydrogen bonding potental might be environment dependent (depends on which SF you are using), and if your residue stripping makes all those residues unburied you'll get different results.
Stripping irrelevant _atoms_ is very very hard, Rosetta only lets you work with whole residues without great effort.
One option you may have is to use the residue_energy_breakdown application (https://www.rosettacommons.org/docs/latest/application_documentation/analysis/residue-energy-breakdown ). This won't do the whole suite of things that the InterfaceAnalyzer does, but it will let you see the energy of interactions between specific pairs of residues. (These energies would correspond to dG cross)
Another thing to note is that because the energy functions of GROMACS and Rosetta are different, structures that are good-scoring by GROMACS might be terrible by Rosetta energy, and vice-versa. You might need to do a short pre-relaxation of the structures in order to get decent Rosetta energies. (https://www.rosettacommons.org/docs/latest/rosetta_basics/preparation/preparing-structures#relax-with-all-heavy-atom-constraints-protocol ) It might not be strictly necessary, so you can try without first, but if you get really bad energies, try the relax to see if it helps.