Problem with a ZINC15 ligand ZINC000170910319
Closed this issue · 2 comments
Hi,
when I use quickvina2 with the ligand ZINC000170910319 I receive the following:
$ qvina2 --config docking_conf_vina_1.txt
############################################################################
# If you used Quick Vina 2 in your work, please cite: #
# #
# Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, and Chee-Keong Kwoh,#
# Fast, Accurate, and Reliable Molecular Docking with QuickVina 2, #
# Bioinformatics (2015), doi: 10.1093/bioinformatics/btv082 #
# #
# You are also encouraged to cite Quick Vina 1: #
# Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong #
# Kwoh, Yew Soon Ong, #
# QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for#
# Global Optimization, #
# IEEE/ACM Transactions on Computational Biology and Bioinformatics,vol.9, #
# no. 5, pp. 1266-1272, Sept.-Oct. 2012, doi: 10.1109/TCBB.2012.82 #
# #
# and original 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 #
############################################################################
Output will be ./zinc15_ligs_1/ZINC000170910319_out.pdbqt
Detected 32 CPUs
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 all works fine as can be seen fron the following:
$ 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, #
# 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
It is possible to fix this?
Thanks.
Saverio
Hi,
the pdbqt converted file that gives the problem is:
ZINC000170910319.pdbqt.txt
Thanks.
Saverio
QVina depends on Vina 1.1.2.
which does not know the new (expanded) forcefield. If you like to compile the new definitions file and submit a pull request, it would be highly appreciated