Hydrogen atom numbering

GROMACS version:2020.4
GROMACS modification: Yes/No No
Here post your question If I use pdb2gmx to generate a .gro file hydrogens are added with a number at the end, for example: HH31, HH32, HH33. However, when I use the same command to generate a .pdb file with hydrogens, the naming convention changes to: 1HH3, 2HH3, 3HH3, etc. How can I get pdb2gmx to add numbers to the end and not to the beginning of the H atoms?

I am not 100% sure, but it seems that you hit an issue, that it was solved in 2021 see
Do you have the same issue with 2021 version?
Best regards


Thanks for your reply. I can’t see the details of this issue, but I was using 2020.4.

I think that I had done this before with no problem using 2020.3, so perhaps this bug was introduce in 2020.4.

I will upgrade my gromacs version and hopefully this issue will disappear.

Meanwhile, it is easy to fox this with an editor 😊.

Best regards,


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