diff --git a/pdb2pqr/config.py b/pdb2pqr/config.py
index f3c6094..a85e00d 100644
--- a/pdb2pqr/config.py
+++ b/pdb2pqr/config.py
@@ -5,6 +5,13 @@
 VERSION = __version__
 
 
+#: Options for PROPKA that PDB2PQR cannot handle
+IGNORED_PROPKA_OPTIONS = [
+    "thermophiles", "chains", "alignment", "mutations", "mutator",
+    "mutator_options", "reuse_ligand_mol2_file", "keep_protons",
+    "protonate_all"
+]
+
 #: How to format PDB2PQR title in output
 TITLE_STR = f"PDB2PQR v{VERSION}: biomolecular structure conversion software."
 
diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py
index e886801..17bd910 100644
--- a/pdb2pqr/main.py
+++ b/pdb2pqr/main.py
@@ -26,7 +26,7 @@
 from .ligand.mol2 import Mol2Molecule
 from .utilities import noninteger_charge
 from .config import VERSION, TITLE_STR, CITATIONS, FORCE_FIELDS
-from .config import REPAIR_LIMIT
+from .config import REPAIR_LIMIT, IGNORED_PROPKA_OPTIONS
 
 
 _LOGGER = logging.getLogger(f"PDB2PQR{VERSION}")
@@ -279,6 +279,13 @@ def check_options(args):
     :type args:  argparse.Namespace
     :raises RuntimeError:  silly option combinations were encountered.
     """
+    for option in IGNORED_PROPKA_OPTIONS:
+        if option in args:
+            _LOGGER.warn(
+                f"PROPKA option '{option}' is not processed correctly by "
+                f"PDB2PQR. Ignoring."
+            )
+            args.__dict__.pop(option)
     if (args.ph < 0) or (args.ph > 14):
         err = (
             f"Specified pH ({args.ph}) is outside the range "