open file in "w" mode: IOError: [Errno 2] No such file or directory

Since you don't have a 'starting' slash, your python script is looking for this file relative to the current working directory (and not to the root of the filesystem). Also note that the directories leading up to the file must exist!

And: use os.path.join to combine elements of a path.

e.g.: os.path.join("dir", "dir2", "dir3", "myfile.ext")

You'll see this error if the directory containing the file you're trying to open does not exist, even when trying to open the file in w mode.

Since you're opening the file with a relative path, it's possible that you're confused about exactly what that directory is. Try putting a quick print to check:

import os

curpath = os.path.abspath(os.curdir)
packet_file = "%s/%s/%s/%s.mol2" % ("dir", "dir2", "dir3", "some_file")
print "Current path is: %s" % (curpath)
print "Trying to open: %s" % (os.path.join(curpath, packet_file))

packetFile = open(packet_file, "w")

I had the same error, but in my case the cause was, under Windows, a path longer than ~250 characters.