When I run grompp in gromacs to generate tpr file, I get this error :"Group referenced in the .mdp file was not found in the index file.". I checked the mdp file, and I realize that the group protein is the unmatched one, since when I replace it to SOL or NA, it is not a problem. In my .top file, I have Protein, Protein2, Protein3, Protein4 as different molecules that represent the different chains in the transmembrane helical bundle. Although, the index file has only one protein group listed as Protein , there are four .itp files, in this format :
[ moleculetype ]
; Name nrexcl
Protein2 3
how can I resolve the Protein issue in the mdp or index file?
thank you
The only valid names are [moleculetypes] or group names in the index file. The index file will contain "Protein" as a default group encompassing all atoms identified as protein, and all [moleculetypes] should be additional available groups. But without seeing your .mdp file and a listing of the groups in the index file, it's impossible to say what the problem is.
pull_group1_name = NA
pull_group2_name = NA
This accomplishes nothing.
pull = umbrella
is invalid. It should be "pull = yes" in version 5.1 (because you set the pull type on a per-coordinate level, which you have set as pull_coord1_type = umbrella).
Thank you Justin, I had the redundant NA as a test, I reran with pull = yes , and I get this now, which I got before, hence my confusion:
"ERROR 1 [file umbrella.mdp, line 65]:
Invalid enum 'yes' for variable pull, using 'no'
Next time use one of: 'no' 'umbrella' 'constraint' 'constant-force'"
What puzzles me the most the fact that there are only 64 lines in the mdp file!!!
Well, then you have a mixture of settings for different GROMACS versions. There have been a lot of changes in the pull code between 4.6, 5.0, and 5.1. My comment above assumes the latest version (5.1); you will have to adjust as needed for whatever version you are using. If you want help troubleshooting the original problem, you need to provide the files that actually trigger the error, otherwise it's a waste of time to comment on something unrelated.
thank you Justin, I realized I was using version 4.6, I am switching to 5.0, and I will use your very helpful suggestions. Hopefully, it works.
I have the simillar question:
When I run grompp in gromacs to generate tpr file, I get this error :"Group referenced in the .mdp file was not found in the index file.".
These are my .mdp file and my index.ndx file. This is my command:
$gmx grompp -f md2-1.mdp -c nvt.gro -n index.ndx -t nvt.cpt -p topol.top -o md2.tpr -maxwarn 2
Could anyone give me some help? Thank you so much!
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running