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

User discussions
1

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.

gromacs_make_ndx_bug
gromacs_make_ndx_bug3865×1944 1.31 MB

2

Hi,

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!

3

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: