make_ndx not recognizing different chains
I wanted to use make_ndx to select a subunit of a pentameric ion channel, but in 2019.3 I still get atoms from all subunits. It seems like the program thinks the whole protein is one chain? The selections I used are in input.txt and the outputs from GROMACS 2019.3 and 2018.4 are in output_201?_?.txt respectively. The selections work fine in 2018.4. Note that in 2019.3 I get 5 times the number of atoms compared to 2018.4.
#3 Updated by Cathrine Bergh 3 months ago
- File 12.ions.pdb 12.ions.pdb added
- File posre_Protein_chain_A.itp posre_Protein_chain_A.itp added
- File script.sh script.sh added
Paul Bauer wrote:
@Cathrine, can you also upload sample inputs so I can fully reproduce this to fix the bug?
Hi! Here's a script you can run with the pdb and itp as input, which should reproduce the bug.