GROMACS version:21
As the error suggest while creating index file i should have incorporated Protein_UNL . which is in my case protein_UNK . but i chose this option 1 | 13 (1 for being protein and 13 for ligand(UNK) . Also I added index group 19 water and ions. i believe i provided everything that was mentioned in my nvt.mdp file but still error arrives. Then how to solve this error ??
You simply typed the name wrong in the .mdp file so you’re calling a nonexistent group.
Really appreciate it. Now that you point it out, I understand .
Fatal error:
Group Protein_UNK 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.
i faced the same kind of error while generating npt.tpr file. it says Protein_UNK is not indexed in the index file . But it is indexed. I have attached the photo of my index file. nvt.tpr was generated with the same index file. Anything i am missing here ??
