First of all, you are not iterating over the file properly. You can simply use for b in f: without the .readline() stuff.
Then your code will blow in your face as soon as the filename contains any characters which have a special meaning in the shell. Use subprocess.call instead of os.system() and pass an argument list.
Here's a fixed version:
with open('query.txt', 'r') as f:
for line in f:
line = line.rstrip() # remove trailing whitespace such as '\n'
subprocess.call(['/bin/grep', line, 'my2.txt'])
However, you can improve your code even more by not calling grep at all. Read my2.txt to a string instead and then use the re module to perform the search. In case you do not need a regex at all, you can even simply use if line in my2_content