(backports)

See #407

LDFLAGS were overwritten by mistake by CFLAGS when doing coverage

It should prepend the libplumed.so library with prefix -Wl,
so as not to disturb NAMD makefile. (suggested by @jcphill)

See #407

As of PLUMED 2.4.1, an error is triggered when aligning using a pdb file
with zeros in the last column. I here fix the provided pdb file.

See this:
https://groups.google.com/d/msgid/plumed-users/4e2f69b8-1b2d-4bd3-a2e3-ecdfeef65d77%40googlegroups.com?utm_medium=email&utm_source=footer