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.

Hi, sorry I can’t help you because I have same issues. How is it going? Have you found the solution for this problem?
Thank you very much.

Hey, can you elaborate how did you create the pdb consisting of multiple peptides from a single peptide?