SDF files fail to run using Ligand Index

[xavierchee]

Hello, i used a file containing SDF file path like the following:

./TEMP_sdf_ligands/Z319894772.sdf
./TEMP_sdf_ligands/Z644871422.sdf
./TEMP_sdf_ligands/Z236962782.sdf
./TEMP_sdf_ligands/Z225356194.sdf
./TEMP_sdf_ligands/Z221152452.sdf
./TEMP_sdf_ligands/Z32845729.sdf
./TEMP_sdf_ligands/Z32879865.sdf
./TEMP_sdf_ligands/Z2793291129.sdf
./TEMP_sdf_ligands/Z2793398822.sdf
./TEMP_sdf_ligands/Z608646848.sdf
./TEMP_sdf_ligands/Z3231330333.sdf
./TEMP_sdf_ligands/Z3231230030.sdf
./TEMP_sdf_ligands/Z1598562232.sdf
./TEMP_sdf_ligands/Z1403323503.sdf
./TEMP_sdf_ligands/Z1262485176.sdf

However, i received the following error.

Scoring function : vina
Rigid receptor: ./indata/def.pdbqt
Grid center: X -36.01 Y 25.63 Z 67.49
Grid size : X 22 Y 22 Z 22
Grid space : 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1

Computing Vina grid ... done.
Total ligands: 15
Available Memory = 80804MiB Total Memory = 81228MiB
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
No fragment info, using rigid docking
/jobfs/local/slurm/job47382478/slurm_script: line 19: 298
4469 Segmentation fault (core dumped) /fred/oz241/xchee/sandbox_unidock/Uni-Dock-main/unidock/bin/unidock --receptor ./indata/def.pdbqt --ligand_index sdf_ligand_path.txt --center_x -36.01 --center_y 25.63 --center_z 67.49 --size_x 22 --size_y 22 --size_z 22 --dir ./result/def --exhaustiveness 8 --max_step 20 --num_modes 1 --scoring vina --refine_step 3 --seed 5

Can i have some advice on this?
Thanks!

[caic99]

Hi @xavierchee ,
Which GPU do you use to run the task?

[xavierchee]

NVIDIA A100

If i use this:
#!/bin/bash

#SBATCH --job-name=unidock
#SBATCH --output=unidock.txt

#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=00:05:00
#SBATCH --mem-per-cpu=20G
#SBATCH --gres=gpu:1
#SBATCH --tmp=200G

ml gcc/12.2.0 boost/1.81.0 cuda/12.0.0

ml conda
conda activate conda_vs

/fred/oz241/xchee/sandbox_unidock/Uni-Dock-main/unidock/bin/unidock --receptor ./indata/def.pdbqt --ligand ./TEMP_sdf_li
gands/Z319894772.sdf --center_x -36.01 --center_y 25.63 --center_z 67.49 --size_x 22 --size_y 22 --size_z 22 --dir ./res
ult/def --exhaustiveness 8 --max_step 20 --num_modes 9 --scoring vina --refine_step 3 --seed 5 --max_gpu_memory 10000

it runs but i still get the no fragment found error.

No fragment info, using rigid docking
Computing Vina grid ... done.
WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs.
Performing docking (random seed: 5) ...
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -6.704 0 0
2 -6.645 5.404 8.731
3 -6.505 4.383 7.992
4 -6.479 2.605 8.607
5 -6.329 4.827 7.372
6 -6.314 4.419 5.919
7 -6.005 2.602 8.867
8 -5.965 4.847 6.089
9 -5.955 3.602 8.157

Thanks

[ysyecust]

Hi @xavierchee there may be some problems with the format of the SDF file. If possible, you can show the content of an SDF file.

[kailash-acog]

My issue is same as what @xavierchee mentioned.
Here is the sample sdf file i am passing and it is showing the same error what @xavierchee mentioned.
CHEMBL3770724
RDKit 3D

43 45 0 0 0 0 0 0 0 0999 V2000
4.4898 -1.8637 -1.6462 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9399 -0.8765 -0.6521 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4764 -1.2316 0.4263 O 0 0 0 0 0 0 0 0 0 0 0 0
3.9875 0.4334 -1.0663 N 0 0 0 0 0 0 0 0 0 0 0 0
3.5042 1.5257 -0.2475 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2201 2.1346 -0.8074 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0037 1.2032 -0.8038 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5388 0.8159 0.6006 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7627 0.1594 0.5745 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.9742 0.7912 0.6766 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9776 -0.1607 0.6183 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3478 -1.4272 0.4680 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8259 -2.7495 0.3525 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9207 -3.8061 0.2158 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5517 -3.5630 0.1944 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0500 -2.2629 0.3070 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9639 -1.2043 0.4427 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3868 0.1980 0.7148 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.3077 -0.6114 0.7464 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.6376 1.5594 0.7807 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.6560 2.5507 0.3535 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2284 2.2498 0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6714 -2.4839 -2.0216 H 0 0 0 0 0 0 0 0 0 0 0 0
4.9705 -1.3655 -2.4924 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2333 -2.4932 -1.1497 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3922 0.6535 -1.9673 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2932 2.2856 -0.2516 H 0 0 0 0 0 0 0 0 0 0 0 0
3.3687 1.2012 0.7888 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4006 2.4578 -1.8406 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9793 3.0385 -0.2348 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2118 0.3012 -1.3916 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1878 1.7189 -1.3269 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2452 0.1421 1.0935 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4457 1.7003 1.2410 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8951 -2.9454 0.3735 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2933 -4.8234 0.1307 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1418 -4.3945 0.0947 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0218 -2.0910 0.2980 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.6228 1.7794 0.7210 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.6769 2.5584 -0.7431 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.9885 3.5319 0.7063 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1464 2.4994 1.9122 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5098 2.8639 0.2965 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 9 1 0
9 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
13 14 1 0
14 15 2 0
15 16 1 0
16 17 2 0
11 18 1 0
18 19 2 0
18 20 1 0
20 21 1 0
21 22 1 0
17 9 1 0
22 10 1 0
17 12 1 0
1 23 1 0
1 24 1 0
1 25 1 0
4 26 1 0
5 27 1 0
5 28 1 0
6 29 1 0
6 30 1 0
7 31 1 0
7 32 1 0
8 33 1 0
8 34 1 0
13 35 1 0
14 36 1 0
15 37 1 0
16 38 1 0
20 39 1 0
21 40 1 0
21 41 1 0
22 42 1 0
22 43 1 0
M END
$$$$

[ysyecust]

@xavierchee @kailash-acog Your SDF file is missing the torsion information ”No fragment info, using rigid docking“
Please use this command:

Uni-Dock/unidock_tools/README.md

Line 45 in 83c5b9f

`Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --center_x 9 --center_y -5 --center_z -5 --size_x 20 --size_y 20 --size_z 20 --search_mode balance --dir .`

[zhengh96]

Uni-Dock Tools have been updated. @xavierchee @kailash-acog

Now you can use the following command to do ligand preparation:

Uni-Dock/unidock_tools/README.md

Line 49 in 0f1e30e

`unidocktools ligandprep -l <Input SDF ligand files, use commas to seperate> -sd <output_dir> -bs <batch_size=1200>`

Or you may use the following command to run Uni-Dock with automatically ligand preparing:

Uni-Dock/unidock_tools/README.md

Line 59 in 0f1e30e

`unidocktools unidock_pipeline -r <receptor file> -l <ligand files> -sd <output_dir> -cx <center_x> -cy <center_y> -cz <center_z>`

[xavierchee]

Thank you @zhengh96 we will try it out and let u know!

Just a comment,

• ideally, the software would be able to take a multi-ligand SDF file and then process them and then output a sanitized multi-ligand SDF file. From what i read from the unidock tools, i need to first split the ligands into individual files before specifying the path for each ligand. This going to cause issues for users who are using supercomputers with limited inodes. Additionally, if this is applied for ultra-large virtual screening, this means users have to store billions of small files.

Thanks!