# Urgent: Queries regarding the gromacs file synthesis for DNA-lipid systems

**URL:** <https://gromacs.bioexcel.eu/t/urgent-queries-regarding-the-gromacs-file-synthesis-for-dna-lipid-systems/8308>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [February 9, 2024, 2:07pm UTC](https://gromacs.bioexcel.eu/t/urgent-queries-regarding-the-gromacs-file-synthesis-for-dna-lipid-systems/8308 "2024-02-09T14:07:47Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [February 13, 2024, 7:48am UTC](https://gromacs.bioexcel.eu/t/urgent-queries-regarding-the-gromacs-file-synthesis-for-dna-lipid-systems/8308/2 "2024-02-13T07:48:04Z")

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It looks like the forcefield you’re using doesn’t have a .hdb file specifying the hydrogen bonds for 3CHL. Based on some previous posts ([Please how can i neutralize the system? - #10 by jalemkul](https://gromacs.bioexcel.eu/t/please-how-can-i-neutralize-the-system/2757/10)), you may need to either fix the naming convention for hydrogen atoms in the pdb file to match the forcefield or design your own .hdb file to add to the forcefield ([https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html#hydrogen-database](https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html#hydrogen-database))

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