To automate the process

1. first download the PDB files with the holo logand.

2. open the pdb in the pymol and select the ligand ( go to the wizard and select the measurment, them you can select the center of the compound and them select the lable to know the center geometry (X Y Z) then you can Export the ligand as l.pdb and receptor as r.pdb)

3. open the autodock tools

4. continue the process with this manual ![[dock.png]]

5. so now we docked the validation. we have some files ( r.pdbqt, r.dpf , r.gpf). for the next automated pathway we use, autosmiles2dock scripts.

6. copy 2 files to the directory ( prepare_ligands.py and dock_all_logands.sh ) and after chmod +x "name of the scripts" you can run them via terminal.

Important

be careful

7. ! the ligand should save as smiles in a .txt format sth like

CCN(CC)C(=O)N1CCN(C)CC1 DIETHYLCARBAMAZINE
O=C(C1CCCCC1)N1CC(=O)N2CCc3ccccc3C2C1 PRAZIQUANTEL

change the .dpf and .gpf

8. so you need to copy the r.dpf, r.gpf. after copy them to the directory you should import some changes to thoes files. so open them in some editor and import the changes like this.

|r.dpf changes:

ligand_types A C HD N NA OA SA P S Cl F Br I
fld r.maps.fld
map r.A.map
map r.C.map
map r.HD.map
map r.N.map
map r.NA.map
map r.OA.map
map r.SA.map
map r.P.map
map r.S.map
map r.Cl.map
map r.F.map
map r.Br.map
map r.I.map

|r.gpf changes :

receptor_types A C HD N NA OA SA P S Cl F Br I
ligand_types   A C HD N NA OA SA P S Cl F Br I
receptor receptor.pdbqt
gridfld receptor.maps.fld
map r.A.map
map r.C.map
map r.HD.map
map r.N.map
map r.NA.map
map r.OA.map
map r.SA.map
map r.P.map
map r.S.map
map r.Cl.map
map r.F.map
map r.Br.map
map r.I.map

9. so you are free to run the ./dock_all_ligand.sh in your terminal.

have fun mate amrqhz