Revert "Fix run_stepwise.sh: optimize scan endpoint before path-opt"

This reverts commit 6911e2e.

Author: t-0hmura

examples/methyltransferase/run_stepwise.sh

@@ -16,28 +16,25 @@ mlmm opt -i r_layered.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 01_op
 # Step 5: 1D bond scan (CS1 of SAM 359 – C8 of PHN 360, target 1.3 Å)
 mlmm scan -i 01_opt_init/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 -s "[('SAM 359 CS1','PHN 360 C8',1.3)]" --out-dir 02_scan
 
-# Step 6: Optimize scan endpoint (product candidate)
-mlmm opt -i 02_scan/stage_01/result.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 02b_opt_scan_end
+# Step 6: Path optimization (Growing String Method)
+mlmm path-opt -i 01_opt_init/final_geometry.pdb 02_scan/stage_01/result.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 03_path_opt
 
-# Step 7: Path optimization (Growing String Method)
-mlmm path-opt -i 01_opt_init/final_geometry.pdb 02b_opt_scan_end/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 03_path_opt
-
-# Step 8: TS optimization
+# Step 7: TS optimization
 mlmm tsopt -i 03_path_opt/hei.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 04_tsopt
 
-# Step 9: IRC
+# Step 8: IRC
 mlmm irc -i 04_tsopt/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 05_irc
 
-# Step 10: Optimize IRC forward endpoint
+# Step 9: Optimize IRC forward endpoint (use single-frame endpoint, not trajectory PDB)
 mlmm opt -i 05_irc/forward_last.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 06_opt_fwd --thresh baker
 
-# Step 11: Optimize IRC backward endpoint
+# Step 10: Optimize IRC backward endpoint
 mlmm opt -i 05_irc/backward_last.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 07_opt_bwd --thresh baker
 
-# Step 12: Frequency analysis (R, TS, P)
+# Step 11: Frequency analysis (R, TS, P)
 mlmm freq -i 06_opt_fwd/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 08_freq_reac
 mlmm freq -i 04_tsopt/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 09_freq_ts
 mlmm freq -i 07_opt_bwd/final_geometry.pdb -l "SAM:1,PHN:-1" --parm complex.parm7 --out-dir 10_freq_prod
 
-# Step 13: Energy diagram (replace placeholder values with actual relative energies)
+# Step 12: Energy diagram (replace placeholder values with actual relative energies)
 mlmm energy-diagram -i "[0, 15.6, -43.7]" -o energy_diagram.png --label-x R TS P