I would like to know what does the value '36 1' or '41 1' that we find in the first line of the .str file correspond to ?
Please be a bit more specific. CHARMM is agnostic regarding filenames, so a file that you name pretty.str, I might call ugly.pdb and they could contain the same data, to be used in the same way by CHARMM (in CHARMM you always have to provide the full filename when you read a dataset) So, is this .str file you refer to a trajectory file, an output file, a coordinate file or perhaps something else?
Stream files follow the same rules as any other charmm input. One of those rules is the ability to embed data structures, using the file structure required, to read coordinates, residue sequences, or in this case, an RTF with residue topology descriptions. The distributed toppar_*.str files that extend the CHARMM force field with additional molecules use this feature. See the 'rtop' info file for a complete description of the RTF format.