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PostPosted: Tue Jul 04, 2017 11:41 am 
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Joined: Tue Jul 04, 2017 10:04 am
Posts: 2
Hi,

I have installed vina and ADT on ubuntu. Please see the warning in RED colour.

swig/python detected a memory leak of type 'BHtree *', no destructor found.


Is this effect the results? Please see the results as well at the end of post. Even if results are correct I am worried that this will slow down vina if I use it for multiple ligands against a receptor.

Vina 1.1.2
ADT 1.5.7
Python 2.7.6

Input Files downloaded from
http://vina.scripps.edu/vina_tutorial.zip

Installing ADT on Ubuntu
sudo apt-get update
sudo apt-get install autodocktools

Installing Autodock Vina on Ubuntu
sudo apt-get update
sudo apt-get install autodock-vina

Preparing receptor file for Docking i.e. from abc.pdb to abc.pdbqt
python /usr/share/pyshared/AutoDockTools/Utilities24/prepare_receptor4.py -A hydrogens -r protein.pdb

Preparing ligand file for Docking i.e. from abc.pdb to abc.pdbqt
python /usr/share/pyshared/AutoDockTools/Utilities24/prepare_ligand4.py -l ligand.pdb

Preparing conf.txt
http://vina.scripps.edu/manual.html#features

Issues while preparing receptor and ligand
swig/python detected a memory leak of type 'BHtree *', no destructor found.
adding gasteiger charges to peptide

Running AutoDock Vina for screening
vina --receptor protein.pdbqt --ligand ligand.pdbqt --config conf.txt

Output
#################################################################
# If you used AutoDock Vina in your work, please cite: #
# #
# 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 #
# #
# Please see http://vina.scripps.edu for more information. #
#################################################################

Output will be ligand_out.pdbqt
Detected 4 CPUs
Reading input ... done.
Setting up the scoring function ... done.
Analyzing the binding site ... done.
Using random seed: -2144862673
Performing search ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
done.
Refining results ... done.

mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 0.0 0.000 0.000
2 0.0 11.544 13.526
3 0.0 5.263 10.734
4 0.0 6.911 8.880
5 0.0 8.371 12.872
6 0.0 5.632 9.816
7 0.0 6.030 7.430
8 0.0 8.314 12.461
9 0.0 7.929 10.975
Writing output ... done.


Regards,
Laeeq


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