different atom number error message

package/AUTHORS

@@ -118,6 +118,8 @@ Chronological list of authors
 2019
   - Ninad Bhat
   - Fenil Suchak
+  - Yibo Zhang
+
 
 External code
 -------------

package/CHANGELOG

@@ -97,6 +97,8 @@ Fixes
     Timestep.dimensions for all Universes and Readers (Issue #2190, PR #2213)
   * Fixed analysis.nucleic.hydroxyl() function: correctly recognize the
     2'-hydroxyl hydrogen H2'; gave wrong results (Issue #2218)
+  * A clear message that the .pdb universe cannot contain a different number of
+    atoms from frame to frame (Issue #1998, PR #2219)
 
 Deprecations
   * analysis.polymer.PersistenceLength no longer requires the perform_fit()

package/MDAnalysis/coordinates/PDB.py

@@ -393,14 +393,17 @@ def _read_frame(self, frame):
                                         line[24:33], line[33:40],
                                         line[40:47], line[47:54]]
 
-        # doing the conversion from list to array at the end is faster
-        self.ts.positions = tmp_buf
-
         # check if atom number changed
         if pos != self.n_atoms:
-            raise ValueError("Read an incorrect number of atoms\n"
-                             "Expected {expected} got {actual}"
-                             "".format(expected=self.n_atoms, actual=pos+1))
+            raise ValueError("Inconsistency in file '{}': The number of atoms "
+                             "({}) in trajectory frame {} differs from the "
+                             "number of atoms ({}) in the corresponding "
+                             "topology.\nTrajectories with varying numbers of "
+                             "atoms are currently not supported."
+                             "".format(self.filename, pos, frame, self.n_atoms))
+
+        # doing the conversion from list to array at the end is faster
+        self.ts.positions = tmp_buf
 
         if self.convert_units:
             # both happen inplace

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -894,3 +894,22 @@ def test_write_pdb_zero_atoms():
         with mda.Writer(outfile, ag.n_atoms) as w:
             with pytest.raises(IndexError):
                 w.write(ag)
+
+
+def test_atom_not_match(tmpdir):
+    # issue 1998
+    outfile = str(tmpdir.mkdir("PDBReader").join('test_atom_not_match' + ".pdb"))
+    u = mda.Universe(PSF, DCD)
+    # select two groups of atoms
+    protein = u.select_atoms("protein and name CA")
+    atoms = u.select_atoms(
+        'resid 1 or resid 10 or resid 100 or resid 1000 or resid 10000')
+    with mda.Writer(outfile, multiframe=True, n_atoms=10) as pdb:
+        # write these two groups of atoms to pdb
+        # Then the n_atoms will not match
+        pdb.write(protein)
+        pdb.write(atoms)
+    reader = mda.coordinates.PDB.PDBReader(outfile)
+    with pytest.raises(ValueError) as excinfo:
+        reader._read_frame(1)
+    assert 'Inconsistency in file' in str(excinfo.value)