Boron atoms in AD4.1_bound.dat

[serenafrancisco]

Hello! I am using AutoDock-GPU for virtual screening, I prepared my receptor as it follows:

1. Generated PDBQT file from PDB using ADT GUI (added polar H, computed Kollman charges and then spread charge deficit);
2. At this point, from terminal, I launched this command: python3 write-gpf.py rec.pdbqt -b box_size.txt --mapprefix rec;
3. On the GPF created above, I added the following line at the top: parameter_file AD4.1_bound.dat, where AD4.1_bound.dat was modified by adding B atom parameter at the bottom (atom_par B 3.84 0.155 29.6478 -0.0015 0.0 0.0 0 -1 -1 0).
4. Launched autogrid4 -p rec.gpf -l rec.glg to generate grid maps for each atom type in the ligand, and got these files in my directory:
   • rec.A.map
   • rec.Br.map
   • rec.C.map
   • rec.Cl.map
   • rec.d.map
   • rec.e.map
   • rec.F.map
   • rec.HD.map
   • rec.I.map
   • rec.maps.fld
   • rec.maps.xyz
   • rec.N.map
   • rec.NA.map
   • rec.OA.map
   • rec.P.map
   • rec.S.map
   • rec.SA.map

Then I ran AutoDock-GPU in batch mode (command autodock_gpu_128wi --filelist path/to/ligands.txt --xmloutput 0 --derivtype OX=OA > my.log).

Now, I think I didn't get how to properly use this AD4.1_bound.dat, as Boron atoms keep giving me problems (Error: No map file specified for atom type B in fld and no derived type (--derivtype, -T) either).

I would really appreciate any corrections/advice to the protocol, also regarding the PDBQT preparation. Thank you very much!

[diogomart]

Hello, option ligand_types in the .gpf file determines which maps autogrid will write. These are complemented by map lines in the same order as the atom types in ligand_types.

[serenafrancisco]

Thank you, it worked!