Develop

README.md

@@ -65,3 +65,40 @@ receptor with updated sidechain positions:
 ```bash
 mk_export.py vina_results.pdbqt -j my_receptor.json -s lig_docked.sdf -p rec_docked.pdb
 ```
+
+### Box-only grid generation (no receptor input)
+
+When you only need a docking box (for Vina or visualization) you can now write **just** the box information without providing a receptor file.
+
+**What it does**
+- Writes a Vina-style box file (`.box.txt`) and a PDB to visualize the box (`.box.pdb`).
+- No receptor input required.
+
+**How to use**
+- Choose one of the following to define the box:
+  1) `--box_center X Y Z` **and** `--box_size X Y Z`, **or**
+  2) `--box_enveloping <ligand file>` **and** `--padding <Å>`
+- Provide either `-v/--write_vina_box` (filename optional) or `-o/--output_basename` to set output names.
+
+**Examples**
+
+Explicit center & size (no receptor):
+```bash
+mk_prepare_receptor.py   --box_only   --box_center 10 20 30   --box_size 22 24 26   -o my_target -v
+```
+This writes:
+- `my_target.box.txt` (Vina-style config with center/size)
+- `my_target.box.pdb` (box visualization)
+
+Envelope a ligand file (no receptor):
+```bash
+mk_prepare_receptor.py   --box_only   --box_enveloping ligand.sdf   --padding 6.0   -v my_box.txt
+```
+This writes:
+- `my_box.txt`
+- `my_box.pdb`
+
+**Notes**
+- `--box_only` **cannot** be combined with receptor inputs (`-i/--read_with_prody`, `--read_pdb`, `--read_pqr`).
+- `--write_gpf` is **not** supported in `--box_only` mode.
+- `--box_center_off_reactive_res` requires a receptor and is **not** available in `--box_only` mode.