Zero protein chain atoms while Indexing a tpr file using gmx 2020 make_ndx

GROMACS version: Gromacs 2020.2
GROMACS modification: No

Hello Everyone,

I found a strange thing while working with Gromacs 2020. I have a .tpr file containing the two protein chain A and B. When I was trying to make an index of chain A and chain B using the gromacs 2020 make_ndx program, it shows 0 atoms.

Whereas, when I use the gromacs 2018.1 make_ndx program for the same task, it works and created an index group of protein chain A and chain B.

Please find attached screenshots, one for gromacs 2018 and other while using gromacs 2020. I don’t know whether user forum is a right platform to report this or I need to report this somewhere else. Thank you very much.


Thanks for the report here - the best place to report is

There, it’s also useful to provide the input .tpr file.

This is very useful for the development of GROMACS!

There seem to be some more users facing a similar issue, so I went ahead with creating an issue on gitlab here, where you can follow the progress yourself: