Problem with the ligand ZINC000170910319

[xavgit]

Hi,
I am experimenting a problem with a ligand downloaded from Zinc15 that have been converted to pdbqt.

The problem is the following:

$ vina-gpu+ --config ./docking_conf_1.txt
#################################################################
If you used Vina-GPU in your work, please cite: #
#
Shidi, Tang, Chen Ruiqi, Lin Mengru, Lin Qingde, #
Zhu Yanxiang, Wu Jiansheng, Hu Haifeng, and Ling Ming. #
Accelerating AutoDock VINA with GPUs. ChemRxiv (2021).Print. #
#
DOI 10.26434/chemrxiv-2021-3qvn2-v3 #
#
And also the origin AutoDock Vina paper: #
O. Trott, A. J. Olson, #
AutoDock Vina: improving the speed and accuracy of docking #
with a new scoring function, efficient optimization and #
multithreading, Journal of Computational Chemistry 31 (2010) #
455-461 #
#
DOI 10.1002/jcc.21334 #
#
#################################################################

Using virtual sreening mode

Output will be in the directory ./zinc15_ligs_1_docking_res
Reading input ...

Parse error on line 71 in file "./zinc15_ligs_1/ZINC000170910319.pdbqt": ATOM syntax incorrect: "CG0" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.

If I use Vina v1.2.3 with the same receptor and ligand the problem does not appears as can be seen from the output of vina:

$ time vina --config docking_conf_vina_1.txt
AutoDock Vina v1.2.3
#################################################################
If you used AutoDock Vina in your work, please cite: #
#
J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli #
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force #
Field, and Python Bindings, J. Chem. Inf. Model. (2021) #
DOI 10.1021/acs.jcim.1c00203 #
#
O. Trott, A. J. Olson, A
AutoDock Vina: improving the speed and accuracy of docking #
with a new scoring function, efficient optimization and #
multithreading, J. Comp. Chem. (2010) #
DOI 10.1002/jcc.21334 #
#
Please see https://github.com/ccsb-scripps/AutoDock-Vina for #
more information. #
#################################################################

Output will be ./zinc15_ligs_1/ZINC000170910319_out.pdbqt
Scoring function : vina
Rigid receptor: receptor.pdbqt
Ligand: ./zinc15_ligs_1/ZINC000170910319.pdbqt
Grid center: X 112.7 Y 109.3 Z 113.165
Grid size : X 20.71 Y 19.73 Z 16.24
Grid space : 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1

Computing Vina grid ... done.
Performing docking (random seed: -1790117891) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************

mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -9.032 0 0
2 -8.974 2.744 6.242
3 -8.94 1.944 3.354
4 -8.938 1.828 2.786
5 -8.876 2.893 5.2

real 0m41,052s
user 18m34,348s
sys 0m0,868s

Vina with the same receptor and ligand closes its operations successfully.
Obviously the config files contain information suitable to the two programs.
It is possible to fix this problem?
Thanks.

Saverio

[xavgit]

Hi,
the ./zinc15_ligs_1/ZINC000170910319.pdbqt with an added .txt suffix is:

ZINC000170910319.pdbqt.txt
Thanks.

Saverio

[dinghezier]

Hi, sorry, since we are improving on AutoDock Vina and not on AutoDock Vina v1.2.3, we do not support this atomic type.