# Adding a number of small peptides to a box of lipid membrane and water (CHARMM-GUI output) **URL:** \ **Category:** User discussions\ **Created:** [April 16, 2022, 11:17pm UTC](https://gromacs.bioexcel.eu/t/adding-a-number-of-small-peptides-to-a-box-of-lipid-membrane-and-water-charmm-gui-output/4032 "2022-04-16T23:17:01Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![sodiumnitrate](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@sodiumnitrate](https://gromacs.bioexcel.eu/u/sodiumnitrate)\ **Post date:** [April 16, 2022, 11:17pm UTC](https://gromacs.bioexcel.eu/t/adding-a-number-of-small-peptides-to-a-box-of-lipid-membrane-and-water-charmm-gui-output/4032/1 "2022-04-16T23:17:02Z")
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. ---
**Author:** ![Rizkiamaliap0198](https://avatars.discourse-cdn.com/v4/letter/r/a5b964/32.png) [@Rizkiamaliap0198](https://gromacs.bioexcel.eu/u/Rizkiamaliap0198)\ **Post date:** [June 27, 2023, 7:02am UTC](https://gromacs.bioexcel.eu/t/adding-a-number-of-small-peptides-to-a-box-of-lipid-membrane-and-water-charmm-gui-output/4032/2 "2023-06-27T07:02:21Z")
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. ---
**Author:** ![siddhant](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@siddhant](https://gromacs.bioexcel.eu/u/siddhant)\ **Post date:** [September 5, 2023, 5:50am UTC](https://gromacs.bioexcel.eu/t/adding-a-number-of-small-peptides-to-a-box-of-lipid-membrane-and-water-charmm-gui-output/4032/3 "2023-09-05T05:50:59Z")
Hey, can you elaborate how did you create the pdb consisting of multiple peptides from a single peptide? ---
**Author:** ![albayrak](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/albayrak/32/2472_2.png) [@albayrak](https://gromacs.bioexcel.eu/u/albayrak)\ **Post date:** [May 13, 2024, 1:59pm UTC](https://gromacs.bioexcel.eu/t/adding-a-number-of-small-peptides-to-a-box-of-lipid-membrane-and-water-charmm-gui-output/4032/4 "2024-05-13T13:59:09Z")
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.