Dear all,
I use Gromacs, and I got the following error.
group Protein_chain_A referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index, group names, in which case you must supply an index file to the ‘-n’ option of grompp.
Group names are the same in the mdp file and the top file [moleculetype] Should I create an index file in this case? If yes, how to generate an index file that has 13 groups?
Thank you so much
Dear Amnah Alalmaie
Are you following Justin Lemkul's tutorial?
Yes, you should create an index file. In general all groups that are not explicitly defined in the .top file must be contained in the index file, otherwise GROMACS doesn't know which atoms you are referring to.
To generate an index file use the command (https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html)
gmx make_ndx -f your_structure.gro/pdb/etx -o index.ndx
dear Nicola Piasentin
Thank you so much for your reply!
The problem is all groups are explicitly defined in the .top file! That's why I feel confused!
Dear Amnah Alalmaie
I think in general is always better to have a well define index file. However you are right, the error message seems a bit confusing.
I have little experience in protein simulations, but it is likely that you can do this with smaller molecules (like water, where all are called SOL or TIP3) and not with proteins which are larger and more complex.
Just try to run
gmx make_ndx -f yourstructure.pdb -o index.ndx
and see what are the names of the groups that GROMACS is automatically recognizing. There won't be any Protein_chain_A for sure, most likely because GROMACS is reading at a deeper level your protein and offering you some other more specific groups. Anyway if Protein_chain_A is your whole protein probably you can refer to it as 'Protein', which should be already automatically implemented by GROMACS. However, a properly build index file is easy to make and saves you from a lot of mistakes!
Hope this helps,
Nicola
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