quantumfuture/vina_qf repository overview

This is a special vina version made by Laszlo Fusti-Molnar from QuantumFuture Scientific. It performs special rigid body docking where the protein kept rigid and all ligand conformations comes from an input sdf file that can be made by qfconfsearchDFT.x application. This sdf input file contains accurate QM based geometries for all conformations and sorted based on ab initio DFT-D4 high quality relative energies which are also attached to all conformations as standard sdf tags. Having such quantities allow us the add realistic conformational strain energies to the vina scores which are covering the intermolecular interactions between the protein and the conformations. The result is a sorted overall docking scores based on the sum of vina scores and the DFT-D4 conformation strain energies. The program also produces another output sdf file when we sort all the results based on using only vina scores without DFT-D4 conformation strain energies, this is just for comparison purposes. Here is how to use it:

Having a directory called like test for example there should be 3 input files in that directory: prot.pdb, dockedLigand.sdf and qfConformations.sdf. The first two file names are fixed and cannot be modified and they can be usually obtained from pdb data sites. The dockedLigand.sdf file is used only to locate the approximate center of the active site. The file name of the conformations can be anything but it should be the output of the qfconfsearchDFT.x application. Having these three files in the test directory this is the command to dock all conformers:

docker container run --workdir=/test -v $(pwd):/test quantumfuture/vina_qf vinaAllQF.sh qfConformations.sdf

All the results will go to the qfConformations.dir/Results directory. If the calculations are interrupted just run the same command again and the calculation will continue where it left off. HAVE FUN!