# How can I generate the correct peptide conformation of insulin peptide during topolgy creation? **URL:** \ **Category:** User discussions\ **Created:** [September 28, 2022, 10:39am UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904 "2022-09-28T10:39:26Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![chinmay](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@chinmay](https://gromacs.bioexcel.eu/u/chinmay)\ **Post date:** [September 28, 2022, 10:39am UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/1 "2022-09-28T10:39:26Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I have taken 4INS, pdb file, for insulin peptide. There are two chains linked by disulfide bonds. While I have created the topology file for this peptide both A and B chains are interconnected at residue 7 and residue 8 respectively and the rest part of the B chain is missing from the protein file. Please suggest the solution in which I could do this. Here I have attached the snapshot of both original pdb file (red color) and the peptide file (blue color) after topology creation. ![new](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/66d6028ef838dc280c1a7bd27da3443a09695c82.png) ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [September 30, 2022, 11:44am UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/2 "2022-09-30T11:44:16Z")
Sorry I do not fully understand your questions? Do you want to know how to define S-S bond between 2 chains using pdb2gmx? Or do you ask how to add residues to your pdb file? Thanks \Alessandra ---
**Author:** ![chinmay](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@chinmay](https://gromacs.bioexcel.eu/u/chinmay)\ **Post date:** [September 30, 2022, 2:42pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/3 "2022-09-30T14:42:33Z")
Dear mam, After creating the topology file, the A chain (21AAs) connected to the B chain (30AAs) at residue number 7. So, the rest residues of the B chain are not shown in VMD. Kindly tell me how to get the correct conformation of both chains. Thanks and regards Chinmay ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 4, 2022, 2:32pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/4 "2022-10-04T14:32:09Z")
Hi, VMD is reading pdb or gro files, not topology files. It may be a problem of visualization style. You can try to visualize using the opition style “lines” (for example), you might see all the atoms belonging to the two chains. I saw that atom 7 is CYS, is this residue involved with S-S bridge with the other chain? Then cross check that the S-S bridge is properly recognized by pdb2gmx (-merge all and -ss may be options to be considered). \Alessandra ---
**Author:** ![chinmay](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@chinmay](https://gromacs.bioexcel.eu/u/chinmay)\ **Post date:** [October 7, 2022, 12:50pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/5 "2022-10-07T12:50:25Z")
Yes mam. They are linked through S-S bridge (CYS7-CYS7). Is it causing problems? ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 18, 2022, 4:06pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/6 "2022-10-18T16:06:58Z")
Hi, If you have S-S bridge between two chains, use the option -merge and -ss to generate the topology. For the visualization with VMD, cartoon-style may not work (it will not shown the whole system) Alessandra ---
**Author:** ![chinmay](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@chinmay](https://gromacs.bioexcel.eu/u/chinmay)\ **Post date:** [October 20, 2022, 2:56pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-generate-the-correct-peptide-conformation-of-insulin-peptide-during-topolgy-creation/4904/7 "2022-10-20T14:56:10Z")
Thank you mam.