# Issue with pdb2gmx when peptide is capped **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [January 19, 2025, 1:09pm UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077 "2025-01-19T13:09:44Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![mostafagh98](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mostafagh98/32/4214_2.png) [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Post date:** [January 19, 2025, 1:09pm UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077/1 "2025-01-19T13:09:44Z")
Hi all, I’m encountering an issue when trying to process my peptide with pdb2gmx in GROMACS using the CHARMm36-jul2022.ff force field. Here’s the situation: 1. I created my PDB using AlphaFold 3 and added the N-acetyl and C-amide caps using CHARMM-GUI. Here’s part of the PDB file: REMARK GENERATED BY CHARMM-GUI ([HTTP://WWW.CHARMM-GUI.ORG](HTTP://WWW.CHARMM-GUI.ORG)) V3.7 ON JAN, 04. 2025. JOB REMARK READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE REMARK DATE: 1/ 4/25 4: 4: 8 CREATED BY USER: apache ATOM 1 CAY LYS P 1 -11.293 -1.388 -11.244 1.00 0.00 PROA ATOM 2 HY1 LYS P 1 -10.901 -1.983 -10.392 1.00 0.00 PROA ATOM 3 HY2 LYS P 1 -12.232 -0.883 -10.929 1.00 0.00 PROA ATOM 4 HY3 LYS P 1 -10.534 -0.631 -11.536 1.00 0.00 PROA ATOM 5 CY LYS P 1 -11.570 -2.293 -12.395 1.00 0.00 PROA ATOM 6 OY LYS P 1 -11.897 -3.465 -12.216 1.00 0.00 PROA ATOM 7 N LYS P 1 -11.443 -1.758 -13.623 1.00 87.90 PROA ATOM 8 HN LYS P 1 -11.178 -0.809 -13.777 1.00 0.00 PROA … ATOM 554 N CYS P 30 15.841 2.920 8.144 1.00 90.41 PROA ATOM 555 HN CYS P 30 15.358 3.654 7.673 1.00 0.00 PROA ATOM 556 CA CYS P 30 15.016 1.826 8.664 1.00 88.72 PROA ATOM 557 HA CYS P 30 13.979 2.119 8.595 1.00 0.00 PROA ATOM 558 CB CYS P 30 15.273 0.567 7.848 1.00 81.91 PROA ATOM 559 HB1 CYS P 30 16.250 0.135 8.152 1.00 0.00 PROA ATOM 560 HB2 CYS P 30 15.332 0.841 6.773 1.00 0.00 PROA ATOM 561 SG CYS P 30 13.966 -0.648 8.096 1.00 72.34 PROA ATOM 562 HG1 CYS P 30 14.306 -0.930 9.345 1.00 0.00 PROA ATOM 563 C CYS P 30 15.324 1.554 10.140 1.00 88.13 PROA ATOM 564 O CYS P 30 15.604 0.427 10.508 1.00 81.80 PROA ATOM 565 NT CYS P 30 15.264 2.623 10.979 1.00 0.00 PROA ATOM 566 HT1 CYS P 30 15.456 2.504 11.954 1.00 0.00 PROA ATOM 567 HT2 CYS P 30 15.029 3.526 10.622 1.00 0.00 PROA TER 568 CYS 30 END 2. When I use `-ter` and select “none” for both the N- and C-terminals, I get the following error: Fatal error: There is a dangling bond at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. 3. When I select “none” for the N-terminal and “CT2” for the C-terminal, I get this error instead: Fatal error: Atom CAY in residue LYS 1 was not found in rtp entry LYS with 22 atoms while sorting atoms. Has anyone encountered a similar issue, or could you suggest a solution? Thanks in advance! ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 20, 2025, 4:46am UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077/2 "2025-01-20T04:46:28Z")
CHARMM applies patches by retaining the parent amino acid residue name, so an acetylated N-terminal lysine will still be called LYS. GROMACS cannot handle this case, and requires a distinct residue called ACE that contains the acetylation. The same is true of the C-terminus. You should not have to regenerate a topology after using CHARMM-GUI; it provides you with GROMACS inputs, including the topology provided you selected that option for output. ---
**Author:** ![mostafagh98](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mostafagh98/32/4214_2.png) [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Post date:** [January 20, 2025, 9:35am UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077/3 "2025-01-20T09:35:13Z")
Thank you so much for your response I used the PDB Reader and Manipulator option in CHARMM-GUI, and there is no option available for generating GROMACS input files. If possible, could you kindly suggest an alternative solution? Furthermore, I am studying peptide/DNA interactions as well as DNA/membrane interactions using GROMACS, and I would greatly value your advice on a specific aspect of my simulations. My DNA structure consists of two strands, and I am uncertain about the best way to handle this in my setup. Would it be more appropriate to define the DNA as a single molecule in the topology file and use tools like `pdb2gmx -merge interactive` to merge the strands together, or to treat the DNA strands as separate chains? I want to ensure that I handle periodic boundary conditions properly and avoid any broken molecule appearances in the trajectory. ![charmm-GUI.output](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/54ba19a33c5da0cd3d89e935a8cbfba3e3add5e6.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 20, 2025, 4:25pm UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077/4 "2025-01-20T16:25:46Z")
> [@mostafagh98](#): > > I used the PDB Reader and Manipulator option in CHARMM-GUI, and there is no option available for generating GROMACS input files. If possible, could you kindly suggest an alternative solution? If you build the whole system (including solvation and ions) through step5, you can download everything in GROMACS format. This is the easiest method. > [@mostafagh98](#): > > Furthermore, I am studying peptide/DNA interactions as well as DNA/membrane interactions using GROMACS, and I would greatly value your advice on a specific aspect of my simulations. My DNA structure consists of two strands, and I am uncertain about the best way to handle this in my setup. `pdb2gmx` can handle multiple chains natively. You don’t have to do anything special. > [@mostafagh98](#): > > Would it be more appropriate to define the DNA as a single molecule in the topology file and use tools like `pdb2gmx -merge interactive` to merge the strands together, or to treat the DNA strands as separate chains? > I want to ensure that I handle periodic boundary conditions properly and avoid any broken molecule appearances in the trajectory. Topological merging has no impact on PBC so there’s no need to do this. ---
**Author:** ![mostafagh98](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mostafagh98/32/4214_2.png) [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Post date:** [January 21, 2025, 4:18am UTC](https://gromacs.bioexcel.eu/t/issue-with-pdb2gmx-when-peptide-is-capped/11077/5 "2025-01-21T04:18:34Z")
Thank you for investing your time