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?
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 😊.