My compiler (gcc 4.4.2) was complaining without these lines

src/PDB.h

@@ -4,6 +4,7 @@
 #include "AtomNumber.h"
 #include "Vector.h"
 #include <vector>
+#include <string>
 
 namespace PLMD{
 

src/Tools.h

@@ -8,6 +8,7 @@
 #include <cmath>
 #include <limits>
 #include <algorithm>
+#include <string.h>
 
 namespace PLMD{