Adding a number of small peptides to a box of lipid membrane and water (CHARMM-GUI output)

GROMACS version: 2021.1
GROMACS modification: No

I’m trying to build a system with a lipid membrane in a box of water, and a handful of small peptides (all identical). I am building the system using CHARMM-GUI. As far as I can tell, CHARMM-GUI does not allow me to add multiple proteins to the system. I have tried making a system of only lipid and water, and then adding the peptide in with gmx insert-molecules. However, this seems to require manual editing of the topology file.

I tried creating a system in CHARMM-GUI with one copy of the peptide, thinking that the modification of the topology file would be easier (because the protein would be listed under molecules already and I would have to change the number). However, I then realized I would have to edit the index file by hand as well.

Is there really no clean way of doing this? Wouldn’t it be reasonable to add functionality to insert-molecules such that topology and index files could be used as inputs and be modified?

I suppose I could get coordinates of the peptides from the .gro file resulting from insert-molecules, convert it to .pdb and upload that to CHARMM-GUI and build another membrane system.

I would greatly appreciate if anyone could tell me if there is an obvious and clean way of doing this that I’m missing.

Update: feeding a .pdb file that contains multiple peptides into CHARMM-GUI results in broken peptide topology. I’m guessing CHARMM-GUI treats the whole .pdb file to be one single protein.

Update2: the CHARMM-GUI peptide fragmentation problem goes away if I include the proper TER records in the input .pdb file. At this point, I have been able to build the system and the simulation seems to be running properly. I would still be interested in learning about how to more easily build this system, for future reference.