# PDB 3.0 standardized atom names no updated

**URL:** https://gromacs.bioexcel.eu/t/pdb-3-0-standardized-atom-names-no-updated/4458
**Category:** User discussions
**Created:** [July 13, 2022, 3:17am UTC](https://gromacs.bioexcel.eu/t/pdb-3-0-standardized-atom-names-no-updated/4458 "2022-07-13T03:17:55Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![bjwiley23](https://avatars.discourse-cdn.com/v4/letter/b/c6cbf5/32.png) [@bjwiley23](https://gromacs.bioexcel.eu/u/bjwiley23)
#### Post date: [July 13, 2022, 3:17am UTC](https://gromacs.bioexcel.eu/t/pdb-3-0-standardized-atom-names-no-updated/4458/1 "2022-07-13T03:17:55Z")

</div>

GROMACS version: 2021.2  
GROMACS modification: No

According to Peter at OpenMM Gromacs is supposed to have updated atoms names for the residues in the `aminoacids.trp` topology files however these are still not updated. I downloaded from ftp://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz and for instance for Methoinine MET in the `aminoacids.trp` under `oplsaa.ff` folder the hydrogens are not named correctly. For MET the HB hydrogens should be named HB2 and HB3 as seen here [https://files.rcsb.org/ligands/view/MET.cif](https://files.rcsb.org/ligands/view/MET.cif). But they are still labeled HB1 and HB2. Example from `oplsaa.ff’.

```auto
[MET]
 [atoms]
     N opls_238 -0.500 1
     H opls_241 0.300 1
    CA opls_224B 0.140 1
    HA opls_140 0.060 1
    CB opls_136 -0.120 2
   HB1 opls_140 0.060 2
   HB2 opls_140 0.060 2

```