improved reporting of failed affinity setting

Change-Id: I8a10c524b9d168c29ca587d6328b8d246d287c47
Fixed format error in online manual.

The .gro format indicated a right-aligned residue name, but in
reality the residue name is left-aligned and the atom name in the
next column is right-aligned.  The online manual now reflects this.

Change-Id: I610392c692bf31f962ad069c23d7e55196b64b53
Merge "Fixed format error in online manual." into release-4-6
Merge "improved reporting of failed affinity setting" into release-4-6