Fixed error message for zwitterion residues

Previously, pdb2gmx complained that the residue was
not available as a 'starting' terminus for isolated
residues (usually zwitterions). This is really confusing
when starting terminus residuetypes ARE available. Now
we properly explain there is no type to use the residue
isolated.

Change-Id: I0c9c8328f12e75a5a7ffaa8ea894ff46f8fdfe75
Remove non-functional PowerPC invsqrt.

Also remove remaining Power6-related CMake code now that there is no
Power6 CPU acceleration option.

Fixes #947, see that issue for justification.

Change-Id: I6466f3ca7297f96757097119ee7b10e7e467bfe7
Fixed GMXRC so we are not polluting standard shell variables

csh/tcsh is now detected by looking for the lower-case $shell
variable, which seems to work on all recent platforms, instead
of using the 'set' command (which affected $* and $@ in bash).
Fixes #1044.

Change-Id: I852d075c80e2bf8f81a02932432dd31b3bab7f09
Merge "Remove non-functional PowerPC invsqrt." into release-4-6
Merge "Fixed GMXRC so we are not polluting standard shell variables" into release-4-6
Add missing defines to PKG_CFLAGS

Change-Id: I7e4234cf194f10aba1a16cfa81774b8f1941ca76
add an option to not build the template

Change-Id: Ia85fc9dfbd191ac66cfff2d7b7c815620d800afe
Merge "Fixed error message for zwitterion residues" into release-4-6
Merge "Add missing defines to PKG_CFLAGS" into release-4-6
Merge "add an option to not build the template" into release-4-6
Set CMake module search path at a better time

This needs to be set before project() in order that
toolchain files for cross compilling can use the same
search path. Otherwise, the users has to specify
fully-qualified toolchain files.

Refs #1064

Change-Id: I1f1fb4803c9f0dd2b95d236da1c1858c5ea382f9