Fix modality embedding and stale config names so the checkpoints load with the current code

instructpro2_stage2_ligand.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ce150fbe6d86bbe69abc31364c057be25964fcaadc8c4ddec5dd630dbcb9e6c4
-size 6437029974
+oid sha256:477a760668d6a95ff727f1ee9a8f3bebb446565d86c40a4fb95ac2b34115d4ba
+size 6407555016