diff --git a/pxmeter/input_builder/model_inputs/boltz.py b/pxmeter/input_builder/model_inputs/boltz.py
index 56e185b..ad8a62c 100644
--- a/pxmeter/input_builder/model_inputs/boltz.py
+++ b/pxmeter/input_builder/model_inputs/boltz.py
@@ -17,8 +17,9 @@
 from dataclasses import dataclass
 from pathlib import Path
 
-import yaml
+import gemmi
 
+import yaml
 from pxmeter.constants import DNA, LIGAND, PROTEIN, RNA
 from pxmeter.input_builder.seq import (
     Bond,
@@ -29,6 +30,34 @@
 from pxmeter.utils import int_to_letters
 
 
+def gemmi_replace_seq_3to1(seq: PolymerChainSequence) -> PolymerChainSequence:
+    """
+    Replace pxmeter 3 to 1 letter mapping to gemmi 3 to 1 letter mapping.
+
+    Args:
+        seq: PolymerChainSequence object.
+
+    Returns:
+        PolymerChainSequence object with replaced sequence.
+    """
+    new_sequece = [i for i in seq.sequence]
+    for mod_pos, mod_res_name in seq.modifications:
+        old = new_sequece[mod_pos - 1]
+        new = gemmi.one_letter_code([mod_res_name])[0]
+        if old != new:
+            logging.warning(
+                f"Change {mod_res_name}->{old} to {mod_res_name}->{new} for consistent with boltz (use gemmi.one_letter_code)."
+            )
+            new_sequece[mod_pos - 1] = new
+    return PolymerChainSequence(
+        entity_type=seq.entity_type,
+        sequence="".join(new_sequece),
+        modifications=seq.modifications,
+        ori_entity_id=seq.ori_entity_id,
+        ori_chain_id=seq.ori_chain_id,
+    )
+
+
 @dataclass(kw_only=True)
 class BoltzInput:
     """
@@ -111,9 +140,16 @@ def from_sequences(cls, sequences: Sequences):
         Returns:
             BoltzInput: Constructed BoltzInput object.
         """
+        new_seqs = []
+        for seq in sequences.sequences:
+            if seq.is_polymer():
+                new_seqs.append(gemmi_replace_seq_3to1(seq))
+            else:
+                new_seqs.append(seq)
+
         return cls(
             name=sequences.name,
-            sequences=sequences.sequences,
+            sequences=new_seqs,
             bonds=sequences.bonds,
         )