compound.to_parmed() stopping early in ancestor hierarchy (ancestor override functionality)

[ahy3nz]

For example: level 3 (ancestor) -> level 2 -> level 1 (particle). Level 3 and level 2 are passed to residues arg, so particle adopts the level 2 residue name, not the level 3 residue name. Within the same overall system, level 2 might actually be the desired residue name. This might require an "ancestor override" where residue names located higher up on the hierarchy override the lower ones (so that level 3 is preferred over level 2)

[ctk3b]

Could you give a specific piece of code that reproduces this and what specifically the other option would produce?

[loganguy11]

The issue arose when I was trying to create a .gro file for the Bilayer Builder. In my current mb.Compound hierarchy, some atoms in my DSPC molecules were being labelled improperly. This is because my DSPC is composed of a head group (written as a python class PCHead()) and tail group (PCTails()); the PCTails class is also composed partially of free fatty acids (FFA()).

The problem arises when I instantiate a Bilayer class (at the bottom of attached file bilayer.py) composed of DSPC and FFA molecules. When I create the .gro file (also attached), it can be seen that some of the atoms in the DSPC molecules get assigned to a residue of FFAUA, not DSPC as they should.

We believe the issue is due to lines 1717-8 of compound.py; by looping through atom.ancestors() and breaking the loop as soon as the first ancestor that exists in residues is found, we are failing to account for the possibility that an atom may have more than one ancestor which is contained in residues. The solution would ideally produce, in my case, a .gro file where all atoms in the DSPC molecule are assigned to the correct residue (DSPC, not FFAUA).
bilayer.py.zip
DSPC_0.5_FFAUA_0.5_UA.gro.zip

NOTE: This issue is resolved by simply changing the name attribute of the FFAUA compound when it is added to the DSPC compound, but it could be beneficial to have functionality built into mBuild that prevents users from having to do that in the future.