For many input filenames, the full filename is obtained by looking for the file in the list of directories specified in the TOP variable DIRECTORY. The directories in DIRECTORY are separated by colons (':') (, `dir1:dir2:dir3:...'). DIRECTORY can also contain the current directory (` ' or `./').
The directory prefix for the input atom coordinate filenames is obtained in a similar way, except that ATOM_FILES_DIRECTORY is used instead of DIRECTORY. Moreover, there is an additional mechanism for reading an atom coordinate file that requires specifying the protein code only (see below in Section on coordinate files and derivative data).
The list of directories is not scanned for the input filenames that start with '/'.
In contrast, the INCLUDE_FILE file is looked for in the distribution's $BIN_MODELLER6 directory (equal to $MODINSTALL6/bin directory) in addition to the DIRECTORY directories. This allows for an easy inclusion of the predefined system '__*.top' files by the INCLUDE command.