Hi,

It seems that if one wants to carry out blind docking with QVina-W still needs to supply the centre and dimensions of the search box, is that correct?

Best,

Miro

How do I install QVina on both Windows and Linux? Thanks.

It's not clear from where the uploaded binaries in bin/ come from.

In the makefile, there is two targets all: vina vina_split which I guess corresponds to the binaries in bin/ ?

From where do the other binaries come from?

It would be helpful to have a consolidated repo where every binary each generate using a single Makefile or using CMake for example. I am happy to submit a PR if someone can provide me some guidance.

Can you share some scripts for ligands' and receptor preparation for docking?

Thanks a lot!

Hi,

It would be helpfull to have a release of qvina: On many HPC clusters scientific software is installed with build frameworks (e.g. easybuild), which in turn rely on releases.

It generally helps to have a release with a specific version number, if an issue is to be addressed - at least, when the tool in question is actively maintained.

Best regards,
Christian

If I am not bothered with the gain in computational time, what other advantages shall I expect from QVina 2 over Vina 1.2.0? I am not inclined to think that the increased reliability persists anymore.

qvina is installed, i can see it in my conda environment, but i dont have commandline access to qvina? how can that be? i installed qvina via conda-forge

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

I get this:

g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/local/include -std=c++0x -L/usr/local/lib -L. -o vina main.o visited.o cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o -l boost_system -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options
/usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: ./libstdc++.a(cow-stdexcept.o): in function `std::logic_error::logic_error(std::logic_error const&)':
/usr/src/debug/gcc-7.4.0-1/libstdc++-v3/src/c++11/cow-stdexcept.cc:59: multiple definition of `std::logic_error::logic_error(std::logic_error const&)'; main.o:main.cpp:(.text$_ZNSt11logic_errorC2ERKS_[_ZNSt11logic_errorC2ERKS_]+0x0): first defined here
/usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: ./libstdc++.a(cow-stdexcept.o): in function `std::runtime_error::runtime_error(std::runtime_error const&)':
/usr/src/debug/gcc-7.4.0-1/libstdc++-v3/src/c++11/cow-stdexcept.cc:65: multiple definition of `std::runtime_error::runtime_error(std::runtime_error const&)'; main.o:main.cpp:(.text$_ZNSt13runtime_errorC2ERKS_[_ZNSt13runtime_errorC2ERKS_]+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:47: vina] Error 1

while trying to compile qvina myself.

Hi! What would be the quickest way of computing gradients of the scoring function w.r.t the coordinates of the ligand? More specifically, for a given protein-ligand pair I would like to know what is the gradient, without performing any optimization/search.

Thanks!

What are the differences in these two versions. I searched but cannot find documentation. With testing, qvina2.1 runs slower than qvina02, so there must be some differences.

I followed all the instructions in https://qvina.github.io/compilingQvina2.html

The only changes in Makefile are as below

BASE=/usr/local/Cellar/boost/1.76.0/include/boost/
BOOST_VERSION=1.76.0
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM= -pthread

attached the output of the make command 2021-10-13_qvina2_make.log

Thanks in advance.

how to compile it in Mac (OS: Yosemite)?

I got error:

clang: warning: argument unused during compilation: '-pthread'
clang: warning: argument unused during compilation: '-ansi'
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [vina] Error 1

Thanks

This is my system

GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for i386-apple-darwin11.3.0
boost library version 1.64

Hi,
Thank you for providing us such a great tool. Now vina support batch docking. But qvina-w don't have this feature. Could you please add batch docking feature to the new version of qvina-w? Thus I do not need to initialize every time which cost much time.