diff --git a/src/boltz/data/parse/fasta.py b/src/boltz/data/parse/fasta.py
index 114cf9841..a37b02db0 100644
--- a/src/boltz/data/parse/fasta.py
+++ b/src/boltz/data/parse/fasta.py
@@ -134,5 +134,4 @@ def parse_fasta(  # noqa: C901, PLR0912
         "version": 1,
     }
 
-    name = path.stem
-    return parse_boltz_schema(name, data, ccd, mol_dir, boltz2)
+    return parse_boltz_schema(path, data, ccd, mol_dir, boltz2)
diff --git a/src/boltz/data/parse/schema.py b/src/boltz/data/parse/schema.py
index a10260bc4..4906c47c3 100644
--- a/src/boltz/data/parse/schema.py
+++ b/src/boltz/data/parse/schema.py
@@ -937,7 +937,7 @@ def token_spec_to_ids(
 
 
 def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
-    name: str,
+    path: Path,
     schema: dict,
     ccd: Mapping[str, Mol],
     mol_dir: Optional[Path] = None,
@@ -983,8 +983,8 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
 
     Parameters
     ----------
-    name : str
-        A name for the input.
+    path : Path
+        Path to the input file.
     schema : dict
         The input schema.
     components : dict
@@ -1000,6 +1000,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
         The parsed target.
 
     """
+    name, parent = path.stem, path.parent
     # Assert version 1
     version = schema.get("version", 1)
     if version != 1:
@@ -1110,12 +1111,16 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             msa = items[0][entity_type].get("msa", 0)
             if (msa is None) or (msa == ""):
                 msa = 0
+            if msa != 0:
+                msa = str((parent / msa).resolve())
 
             # Check if all MSAs are the same within the same entity
             for item in items:
                 item_msa = item[entity_type].get("msa", 0)
                 if (item_msa is None) or (item_msa == ""):
                     item_msa = 0
+                if item_msa != 0:
+                    item_msa = str((parent / item_msa).resolve())
 
                 if item_msa != msa:
                     msg = "All proteins with the same sequence must share the same MSA!"
diff --git a/src/boltz/data/parse/yaml.py b/src/boltz/data/parse/yaml.py
index a08b7abf5..26e29ea8e 100644
--- a/src/boltz/data/parse/yaml.py
+++ b/src/boltz/data/parse/yaml.py
@@ -64,5 +64,4 @@ def parse_yaml(
     with path.open("r") as file:
         data = yaml.safe_load(file)
 
-    name = path.stem
-    return parse_boltz_schema(name, data, ccd, mol_dir, boltz2)
+    return parse_boltz_schema(path, data, ccd, mol_dir, boltz2)