AutoDock-Vina
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ccsb-scripps
AutoDock Vina
Dear all, I realized from issue #264 that `--autobox` doesn't set grid size or center in a docking search. But Vina will print the following to standard output whenever it...
==195708== 120 bytes in 5 blocks are definitely lost in loss record 580 of 1,478 ==195708== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==195708== by 0x216113: ScoringFunction::ScoringFunction(scoring_function_choice, std::vector const&) (scoring_function.h:50)...
Fixes leaks reported by valgrind as below (before fix). After fix, this is no longer reported. ==195708== 120 bytes in 5 blocks are definitely lost in loss record 580 of...
I am writing a python script and encountered with a following error: ... v = vina.Vina(sf_name='ad4', verbosity=1, seed=selectedSeed) ... v.set_receptor(rigid_pdbqt_filename=="xxx.pdbqt",flex_pdbqt_filename="yyy.pdbqt") ... ERROR: Only flexible residues allowed with the AD4 scoring...
I wonder what is the unit of vina's map size. Typically the CNN scoring functions only accept box as 20*20*20 A to score, but when I use this size in...
I encountered difficulties while learning **docking with zinc metalloproteins** when using autogrid4 to generate protein_tz.glg from protein_tz.gpf. The error message is shown below, and the version used is attached at...
I have followed the instructions from this tutorial: https://autodock-vina.readthedocs.io/en/latest/docking_hydrated.html. After implementing step 5, I get similar results for vina command but dry,py is not removing 5 water molecules. Its not...
It seems that the directionality of H-bond is not considered according to the code. class vina_non_dir_h_bond : public Potential { public: vina_non_dir_h_bond(fl good_, fl bad_, fl cutoff_) : good(good_), bad(bad_),...
Hi, I am executing the following command: ```bash vina_1.2.5_mac_x86_64 --receptor this_dir_is_empty --center_x 1.2 --center_y -5.5 --center_z -5.1 --size_x 23.7 --size_y 15.1 --size_z 25.2 --ligand ligand.pdbqt --out ligand_out.pdbqt ``` And it...
https://github.com/ccsb-scripps/AutoDock-Vina/blob/d13f9e93e253573b01ffbb28cfd1e2dd26ff9002/src/lib/potentials.h#L471C12-L471C19 Hello! In the referenced line above, `vdw_rij` is unused and could therefore be deleted
