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