# TopologyFiles for non standard nucleotides **URL:** \ **Category:** User discussions\ **Created:** [March 18, 2022, 11:04am UTC](https://gromacs.bioexcel.eu/t/topologyfiles-for-non-standard-nucleotides/3862 "2022-03-18T11:04:15Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Laura.troussicot](https://avatars.discourse-cdn.com/v4/letter/l/ecccb3/32.png) [@Laura.troussicot](https://gromacs.bioexcel.eu/u/Laura.troussicot)\ **Post date:** [March 18, 2022, 11:04am UTC](https://gromacs.bioexcel.eu/t/topologyfiles-for-non-standard-nucleotides/3862/1 "2022-03-18T11:04:15Z")
GROMACS version:2021.4 GROMACS modification: Yes/No Here post your question Hello Gmx community. I am trying to create a topology file for an RNA system containing pseudouridine (and possibly afterwards, other post transcriptional modifications). I successfully built the topology file for the PSU residue and included it in the rtp file of the force field I am using. I also modified accordingly the residue types.dat. My issue concerns the rna.hdb file for adding hydrogens to my system using pdb2gmx. I know I should add 11 hydrogens atoms that gmx finds missing when trying to build the topology file, but I cannot figure out how to properly modify the rna.hdb file for my PSU nucleotide. I would be grateful for any help or explanation concerning the different columns in, and therefore how to modify this file :) Thanks a lot. Laura TROUSSICOT, PhD. ---
**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:** [March 18, 2022, 5:44pm UTC](https://gromacs.bioexcel.eu/t/topologyfiles-for-non-standard-nucleotides/3862/2 "2022-03-18T17:44:37Z")
See [pdb2gmx input files — GROMACS 2022 documentation](https://manual.gromacs.org/documentation/current/reference-manual/topologies/pdb2gmx-input-files.html#hydrogen-database)