change some char to string in gmxpreprocess

change some char to string in gmxpreprocess

Related to #2566 and #2570. As part of the refactoring of
pdb2gmx one thing that becomes clear is that a lot of variables
could have better defined scope and readability could be
improved if some char's are converted to string's. This can
ripple through the code base of gmxpreprocess. I have followed
some of those ripples here and will continue to follow in
later changes.

Change-Id: I0d12704ef27c06a4f64f8d1e8638760c8c7019ae