# \#topology **URL:** https://gromacs.bioexcel.eu/tag/topology/64.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [X2top not generating listed interactions correctly](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593)
**Author:** [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\ **Replies:** 1\ **Last updated:** [July 23, 2026, 1:17pm UTC](https://gromacs.bioexcel.eu/t/x2top-not-generating-listed-interactions-correctly/13593 "2026-07-23T13:17:21Z")
GROMACS version: 2026.1 GROMACS modification: No Hi, I am trying to generate the topology for two refrigerant molecules (1233zd and 1234ze) using gmx x2top. These are my force field files: workflow-refrigerants/examp… --- ## [\`opc.gro\` available on GitHub](https://gromacs.bioexcel.eu/t/opc-gro-available-on-github/13380)
**Author:** [@Ernest\_NH\_Ho](https://gromacs.bioexcel.eu/u/Ernest_NH_Ho)\ **Replies:** 1\ **Last updated:** [April 13, 2026, 11:20am UTC](https://gromacs.bioexcel.eu/t/opc-gro-available-on-github/13380 "2026-04-13T11:20:38Z")
I recently installed the 2026.1 version. Initially, I chose opc water model, but I couldn’t find any opc.gro, so I used tip4p.gro. However, it occasionally returned a “Not enough replaceable solvent molecules”. Clearly… --- ## [How to build Ligand topology](https://gromacs.bioexcel.eu/t/how-to-build-ligand-topology/13142)
**Author:** [@Riya](https://gromacs.bioexcel.eu/u/Riya)\ **Replies:** 2\ **Last updated:** [February 4, 2026, 11:27am UTC](https://gromacs.bioexcel.eu/t/how-to-build-ligand-topology/13142 "2026-02-04T11:27:47Z")
GROMACS version: 2025 GROMACS modification: No Hello everyone, I am new to molecular dynamics simulations and I would like to confirm whether my procedure for building a ligand topology is correct, and how to properly… --- ## [Fatal error: number of coordinates in coordinate file does not match topology file](https://gromacs.bioexcel.eu/t/fatal-error-number-of-coordinates-in-coordinate-file-does-not-match-topology-file/8115)
**Author:** [@tima](https://gromacs.bioexcel.eu/u/tima)\ **Replies:** 7\ **Last updated:** [January 7, 2026, 1:24pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-number-of-coordinates-in-coordinate-file-does-not-match-topology-file/8115 "2026-01-07T13:24:21Z")
GROMACS version: 2021.3 GROMACS modification: While performing Protein-Ligand interaction in Gromacs version 2021 using the command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr. I encountered this… --- ## [Topology files with packmol](https://gromacs.bioexcel.eu/t/topology-files-with-packmol/8525)
**Author:** [@tebg](https://gromacs.bioexcel.eu/u/tebg)\ **Replies:** 6\ **Last updated:** [October 20, 2025, 1:26pm UTC](https://gromacs.bioexcel.eu/t/topology-files-with-packmol/8525 "2025-10-20T13:26:55Z")
GROMACS version: 2023.3 GROMACS modification: Yes Hi all! This may be a very basic question and apologies if so, but if I am building a decanoic acid membrane with packmol (using decanoic acid generated with molefactur… --- ## [Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field](https://gromacs.bioexcel.eu/t/pdb2gmx-fails-residue-mgp-not-found-in-charmm36-force-field/12513)
**Author:** [@madsondeluna](https://gromacs.bioexcel.eu/u/madsondeluna)\ **Replies:** 2\ **Last updated:** [October 5, 2025, 11:34am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-fails-residue-mgp-not-found-in-charmm36-force-field/12513 "2025-10-05T11:34:09Z")
Hello everyone, I am trying to set up a simulation for the eIF4E protein in complex with the 5’ cap analog, m⁷GTP, using the PDB entry 4TPW. In this PDB file, this molecule is assigned the residue name ‘MGP’. My goal i… --- ## [x2top for MINFF](https://gromacs.bioexcel.eu/t/x2top-for-minff/12722)
**Author:** [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Replies:** 0\ **Last updated:** [October 2, 2025, 6:23am UTC](https://gromacs.bioexcel.eu/t/x2top-for-minff/12722 "2025-10-02T06:23:48Z")
I have modified the gmx x2top tool so that it can also be used to generate Gromacs .top or .itp topology files for the MINFF forcefield (for oxides/hydroxides and many (clay)minerals), using simple .n2t files now availab… --- ## [How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?](https://gromacs.bioexcel.eu/t/how-to-generate-topology-and-itp-files-for-succinic-acid-and-zn-in-gromacs-using-opls-aa/12579)
**Author:** [@Samuel\_Reji\_Bits](https://gromacs.bioexcel.eu/u/Samuel_Reji_Bits)\ **Replies:** 0\ **Last updated:** [August 28, 2025, 10:27am UTC](https://gromacs.bioexcel.eu/t/how-to-generate-topology-and-itp-files-for-succinic-acid-and-zn-in-gromacs-using-opls-aa/12579 "2025-08-28T10:27:59Z")
I’m setting up a GROMACS simulation (10 nm box made with PACKMOL) containing water, Zn²⁺, and succinic acid using the OPLS-AA force field. Since succinic acid is not a biomolecule, pdb2gmx shows it as UNL, and external t… --- ## [Modifying topol.top with each step of peptide insertion over membrane from CHARMM-GUI](https://gromacs.bioexcel.eu/t/modifying-topol-top-with-each-step-of-peptide-insertion-over-membrane-from-charmm-gui/12475)
**Author:** [@tanjim\_ibl](https://gromacs.bioexcel.eu/u/tanjim_ibl)\ **Replies:** 2\ **Last updated:** [August 2, 2025, 3:46pm UTC](https://gromacs.bioexcel.eu/t/modifying-topol-top-with-each-step-of-peptide-insertion-over-membrane-from-charmm-gui/12475 "2025-08-02T15:46:33Z")
GROMACS version: 2025.2 GROMACS modification: No I got membrane from charmm-gui and equilibrated it for 5 ns with 4 steps of NVT and 2 steps of NPT. No matter what I do the waters above membrane always shrink. So I dec… --- ## [Does bond order in MOL2 file affect rtp generation and pdb2gmx?](https://gromacs.bioexcel.eu/t/does-bond-order-in-mol2-file-affect-rtp-generation-and-pdb2gmx/12161)
**Author:** [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\ **Replies:** 2\ **Last updated:** [June 5, 2025, 9:11pm UTC](https://gromacs.bioexcel.eu/t/does-bond-order-in-mol2-file-affect-rtp-generation-and-pdb2gmx/12161 "2025-06-05T21:11:53Z")
@hess @jalemkul Hello, I hope this email finds you well. I used a MOL2 file as input in CHARMM-GUI to generate the .rtp file for a non-standard residue in GROMACS. I then used pdb2gmx to generate the topology for th… --- ## [Confusion over RB and Fourier Dihedrals](https://gromacs.bioexcel.eu/t/confusion-over-rb-and-fourier-dihedrals/12174)
**Author:** [@Lois](https://gromacs.bioexcel.eu/u/Lois)\ **Replies:** 0\ **Last updated:** [May 29, 2025, 3:09pm UTC](https://gromacs.bioexcel.eu/t/confusion-over-rb-and-fourier-dihedrals/12174 "2025-05-29T15:09:36Z")
Hi all, I’m slightly lost on the description of the RB and Fourier potentials for proper dihedrals as described in the below link: In equation (200) the Fourier potential is given with parameters F1 to F4, which is t… --- ## [Apply constraints to desire molecules](https://gromacs.bioexcel.eu/t/apply-constraints-to-desire-molecules/11806)
**Author:** [@Neda](https://gromacs.bioexcel.eu/u/Neda)\ **Replies:** 3\ **Last updated:** [March 28, 2025, 2:11pm UTC](https://gromacs.bioexcel.eu/t/apply-constraints-to-desire-molecules/11806 "2025-03-28T14:11:34Z")
GROMACS version: 2021.7 GROMACS modification: Yes/No Dear all, I plan to simulate a mixture of octane and CO₂ using different force fields. In my setup, the bonds in octane should be constrained, while the bonds in CO… --- ## [Novice to simulate antibody-drug-conjugate -- unnatural residues](https://gromacs.bioexcel.eu/t/novice-to-simulate-antibody-drug-conjugate-unnatural-residues/11798)
**Author:** [@Reece\_Wong\_8998](https://gromacs.bioexcel.eu/u/Reece_Wong_8998)\ **Replies:** 1\ **Last updated:** [March 26, 2025, 9:33am UTC](https://gromacs.bioexcel.eu/t/novice-to-simulate-antibody-drug-conjugate-unnatural-residues/11798 "2025-03-26T09:33:19Z")
GROMACS version: 2022 GROMACS modification: No Here post your question: Hi, friends in this Gromacs forum: I am a novice in gromacs, but I can finish MD of glycoproteins using charmmGUI (which is highly novice-friend… --- ## [cGenFF Ligand topology](https://gromacs.bioexcel.eu/t/cgenff-ligand-topology/11732)
**Author:** [@AndreaMx](https://gromacs.bioexcel.eu/u/AndreaMx)\ **Replies:** 0\ **Last updated:** [March 13, 2025, 2:12am UTC](https://gromacs.bioexcel.eu/t/cgenff-ligand-topology/11732 "2025-03-13T02:12:42Z")
GROMACS version: 2023 GROMACS modification: No Hi I am new in this field, I am doing the protein ligand complex tutorial from the website but applied to my protein and ligand of interest . I am in the step of generati… --- ## [How to set the bond constraint of the sidechain in a self-designed peptide](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541)
**Author:** [@Linqy](https://gromacs.bioexcel.eu/u/Linqy)\ **Replies:** 3\ **Last updated:** [February 18, 2025, 5:57am UTC](https://gromacs.bioexcel.eu/t/how-to-set-the-bond-constraint-of-the-sidechain-in-a-self-designed-peptide/11541 "2025-02-18T05:57:18Z")
GROMACS version:2021.3-bioconda GROMACS modification: Yes/No Hello! I’m a big fan of GROMACS and recently I have been researching on a peptide of 30 amino acids which is designed by myself based on the published articl… --- ## [How to perform md simulation on a protein structure which have a ca+ ions](https://gromacs.bioexcel.eu/t/how-to-perform-md-simulation-on-a-protein-structure-which-have-a-ca-ions/11122)
**Author:** [@preena123](https://gromacs.bioexcel.eu/u/preena123)\ **Replies:** 0\ **Last updated:** [January 23, 2025, 7:25am UTC](https://gromacs.bioexcel.eu/t/how-to-perform-md-simulation-on-a-protein-structure-which-have-a-ca-ions/11122 "2025-01-23T07:25:30Z")
I’m a beginner in molecular dynamics (MD) simulations, and I need guidance on how to perform MD simulations with a protein that includes a calcium ion (Ca⁺). My ultimate goal is to perform protein-ligand MD simulations. … --- ## [Chloroform as a solvent in Charmm36 force field](https://gromacs.bioexcel.eu/t/chloroform-as-a-solvent-in-charmm36-force-field/10787)
**Author:** [@mehr](https://gromacs.bioexcel.eu/u/mehr)\ **Replies:** 1\ **Last updated:** [January 16, 2025, 12:57pm UTC](https://gromacs.bioexcel.eu/t/chloroform-as-a-solvent-in-charmm36-force-field/10787 "2025-01-16T12:57:45Z")
GROMACS version: 2022.5 GROMACS modification: No I am interested in using chloroform (CHCl3) as a solvent instead of water in the Charmm36 force field. Unfortunately, I couldn’t find any topology for chloroform and sin… --- ## [Issues with Ligand Topology Creation Using CGENFF and CHARMM-GUI](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932)
**Author:** [@keinerfan](https://gromacs.bioexcel.eu/u/keinerfan)\ **Replies:** 2\ **Last updated:** [January 7, 2025, 2:34pm UTC](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932 "2025-01-07T14:34:42Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Dear GROMACS Forum, I am encountering issues with creating ligand topologies for my simulations. When I attempt to upload my ligands to generate p… --- ## [Atom OXT in residue GLN 336 was not found in rtp entry GLN with 17 atoms while sorting atoms](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-gln-336-was-not-found-in-rtp-entry-gln-with-17-atoms-while-sorting-atoms/10857)
**Author:** [@pengwu](https://gromacs.bioexcel.eu/u/pengwu)\ **Replies:** 3\ **Last updated:** [December 19, 2024, 1:25pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-gln-336-was-not-found-in-rtp-entry-gln-with-17-atoms-while-sorting-atoms/10857 "2024-12-19T13:25:23Z")
GROMACS version:2022.2 GROMACS modification: Yes/No Here post your question ： After performing protein-protein molecular docking, I want to try molecular dynamics simulations. To make it easier to distinguish, I chang… --- ## [High Penalty Score in CGENFF topology](https://gromacs.bioexcel.eu/t/high-penalty-score-in-cgenff-topology/10821)
**Author:** [@onuratesss98](https://gromacs.bioexcel.eu/u/onuratesss98)\ **Replies:** 0\ **Last updated:** [December 15, 2024, 4:19pm UTC](https://gromacs.bioexcel.eu/t/high-penalty-score-in-cgenff-topology/10821 "2024-12-15T16:19:30Z")
GROMACS version:2021.4 GROMACS modification: No Hi, I’m currently learning how to do MD analysis by myself and after following the instructions on the Gromacs tutorial page, I wanted to do a MD analysis by myself but t… --- ## [Applying constraints to different molecules in a same system](https://gromacs.bioexcel.eu/t/applying-constraints-to-different-molecules-in-a-same-system/10586)
**Author:** [@abhishekchemistry](https://gromacs.bioexcel.eu/u/abhishekchemistry)\ **Replies:** 0\ **Last updated:** [November 19, 2024, 5:56pm UTC](https://gromacs.bioexcel.eu/t/applying-constraints-to-different-molecules-in-a-same-system/10586 "2024-11-19T17:56:33Z")
GROMACS version: 2019.6 GROMACS modification: Yes/No Dear Community, I am trying to simulate a hydrophobic polymer in Madrid-2019 sulfate salt with TIP4P/2005 water. My polymer has 32 monomers connected via bonds and… --- ## [Trouble with CGenFF and Ligand Topology in GROMACS](https://gromacs.bioexcel.eu/t/trouble-with-cgenff-and-ligand-topology-in-gromacs/10376)
**Author:** [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\ **Replies:** 0\ **Last updated:** [October 19, 2024, 8:03am UTC](https://gromacs.bioexcel.eu/t/trouble-with-cgenff-and-ligand-topology-in-gromacs/10376 "2024-10-19T08:03:59Z")
GROMACS version: 2023 GROMACS modification: No Python version: 3.12.2 Hi everyone, I come from a biology background, so my knowledge of programming is limited. I’m doing the protein-ligand tutorial from the mdtutorial… --- ## [Help with "Inconsistent Residue Types" Error](https://gromacs.bioexcel.eu/t/help-with-inconsistent-residue-types-error/10255)
**Author:** [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Replies:** 1\ **Last updated:** [September 30, 2024, 8:24am UTC](https://gromacs.bioexcel.eu/t/help-with-inconsistent-residue-types-error/10255 "2024-09-30T08:24:01Z")
Hello everyone, I am encountering a consistent issue when running simulations with both the Amber99SB-ILDN and Charmm36 force fields. Despite defining the C- and N-terminals of my protein for Charmm36, I receive the fol… --- ## [Error in using cgenff for ligand topology, ligand.str missed bond information](https://gromacs.bioexcel.eu/t/error-in-using-cgenff-for-ligand-topology-ligand-str-missed-bond-information/10246)
**Author:** [@zansia](https://gromacs.bioexcel.eu/u/zansia)\ **Replies:** 1\ **Last updated:** [September 27, 2024, 9:20am UTC](https://gromacs.bioexcel.eu/t/error-in-using-cgenff-for-ligand-topology-ligand-str-missed-bond-information/10246 "2024-09-27T09:20:23Z")
GROMACS version: 2023.3 GROMACS modification: No Here post your question Hi I want to use cgenff for making ligand topology but i’ve noticed .str file that returns as output is missed information about bonds which i… --- ## [Error in CGenFF: "No valid resonance structure found"](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235)
**Author:** [@asoorni](https://gromacs.bioexcel.eu/u/asoorni)\ **Replies:** 3\ **Last updated:** [September 26, 2024, 8:59am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235 "2024-09-26T08:59:49Z")
Hello, I’m new to docking and I’m trying to create a topology file for Cyanidin 3-glucoside as a ligand using CGenFF. I’ve added hydrogens and sorted my mol2 file, but I’m getting a warning “no valid resonance structure … --- ## [Protein with Ion cofactors](https://gromacs.bioexcel.eu/t/protein-with-ion-cofactors/10108)
**Author:** [@adextre](https://gromacs.bioexcel.eu/u/adextre)\ **Replies:** 1\ **Last updated:** [September 6, 2024, 6:51am UTC](https://gromacs.bioexcel.eu/t/protein-with-ion-cofactors/10108 "2024-09-06T06:51:07Z")
GROMACS version: 2024.1 GROMACS modification: No Hello everyone, I’m trying to simulate a protein dimer which has 3 calcium ions at a specific linker site. I can easily place the calciums where I want them in my PDB f… --- ## [Issues Running GROMACS with Amber Force Field - Seeking Guidance](https://gromacs.bioexcel.eu/t/issues-running-gromacs-with-amber-force-field-seeking-guidance/9969)
**Author:** [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Replies:** 1\ **Last updated:** [August 26, 2024, 3:49pm UTC](https://gromacs.bioexcel.eu/t/issues-running-gromacs-with-amber-force-field-seeking-guidance/9969 "2024-08-26T15:49:09Z")
Dear GROMACS Community, I hope this message finds you well. I’ve been successfully running simulations with the CHARMM force field but have recently started working with the Amber force field (AMBER99SB-ILDN for protein… --- ## [Problem in generating topology file for nanoporous MoS2 membrane](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-for-nanoporous-mos2-membrane/9611)
**Author:** [@Pragin](https://gromacs.bioexcel.eu/u/Pragin)\ **Replies:** 0\ **Last updated:** [July 10, 2024, 10:42am UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-for-nanoporous-mos2-membrane/9611 "2024-07-10T10:42:41Z")
GROMACS version: 2021.4 GROMACS modification: No I am working on a project related to water desalination through nanoporous membranes. I have been trying to set up a system with a nanoporous membrane in the middle of t… --- ## [Topol.top file not generating](https://gromacs.bioexcel.eu/t/topol-top-file-not-generating/9586)
**Author:** [@VeronicaKruk](https://gromacs.bioexcel.eu/u/VeronicaKruk)\ **Replies:** 1\ **Last updated:** [July 7, 2024, 3:33pm UTC](https://gromacs.bioexcel.eu/t/topol-top-file-not-generating/9586 "2024-07-07T15:33:31Z")
GROMACS version: gmx pdb2gmx, version 2020-rc1-MODIFIED GROMACS modification: Yes While trying to generate the force field for LYSOZYME (AKI1) I am receiving the following error message: Program: gmx pdb2gmx, vers… --- ## [.gro no match .top](https://gromacs.bioexcel.eu/t/gro-no-match-top/9582)
**Author:** [@C18](https://gromacs.bioexcel.eu/u/C18)\ **Replies:** 3\ **Last updated:** [July 5, 2024, 9:09pm UTC](https://gromacs.bioexcel.eu/t/gro-no-match-top/9582 "2024-07-05T21:09:54Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi I have a .gro file of a protein from which on pymol I mutated a residue from GLN to ALA. Using the same topology (to avoid doing the parameteri… [Next page](https://gromacs.bioexcel.eu/tag/topology/64.md?match_all_tags=true&page=1&tags%5B%5D=topology)