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

User discussions
1

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.

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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.

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

4

Hi! I am trying to do the same thing as you did. I somehow managed the add 6 peptides on the extracellular part of the membrane but here is the issue; when I solvate the system, it adds water molecules on the X and Y axes as well. So I thought I should create a rectangular box that adds space just in the Z axis, not X and Y. But I cannot figure out how to do that. If you can help with this, I would appreciate it.