Fix segfault on calling `make_ndx` without structure file

Fix segfault on calling `make_ndx` with only an index file input (no structure file).

Cause: Migration away from `t_blocka` in d7fca736 was not fully equivalent to previous code - natoms was not set. (`+1` comes from [this](d7fca736) )

Not sure how to emulate inputs at the interactive prompt to add a test for this.

Fixes #4717

docs/release-notes/2023/2023.1.rst

@@ -33,6 +33,13 @@ Fix crash in ``gmx solvate`` when using solvent box in PDB format
 Now a PDB file can be passed to the ``-cs`` option in ``gmx solvate``.
 In previous releases (since at least 2016) this lead to a segfault.
 
+Fix creating index file from another index file
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+``gmx make_ndx`` can again accept an index file alone as input, without associated structure file.
+
+:issue:`4717`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/gromacs/tools/make_ndx.cpp

@@ -1376,19 +1376,20 @@ static void edit_index(int                      natoms,
     sfree(index2);
 }
 
-static int maxAtomIndex(gmx::ArrayRef<const IndexGroup> indexGroups)
+//! Find the number of atoms in the system implied by the largest atom index
+static int impliedNumberOfAtom(gmx::ArrayRef<const IndexGroup> indexGroups)
 {
-    int maxAtom = -1;
+    int maxAtomIndex = -1;
 
     for (const auto& indexGroup : indexGroups)
     {
         for (const int a : indexGroup.particleIndices)
         {
-            maxAtom = std::max(maxAtom, a);
+            maxAtomIndex = std::max(maxAtomIndex, a);
         }
     }
 
-    return maxAtom;
+    return maxAtomIndex + 1;
 }
 
 int gmx_make_ndx(int argc, char* argv[])
@@ -1500,8 +1501,8 @@ int gmx_make_ndx(int argc, char* argv[])
 
     if (!bNatoms)
     {
-        const int maxAtom = maxAtomIndex(indexGroups);
-        printf("Counted atom numbers up to %d in index file\n", 1 + maxAtom);
+        natoms = impliedNumberOfAtom(indexGroups);
+        printf("Deducing %d atoms in the system from indices in the index file\n", natoms);
     }
     edit_index(natoms, &atoms, x, &indexGroups, bVerbose);