I want to make index file according to atom type. I run gmx make_ndx -f .gro -o .ndx . Then I went with the option ‘t’. But I am getting an error “need a run input file to select atom types”. Can anyone help me with this? what does it mean?
It means you need a .tpr file (which is also called a “run input file”) because it is the only file that associates topological information (atom types) with global atom numbers. Coordinate files only contain residue and atom names, thus you can only make selections based on these properties with make_ndx.