Obtaining lowest binding affinity and extracting the residue

Hi, I have 2 questions about VirtualFlow that I am trying to resolve.

  1. Is it possible to obtain the 10 LOWEST binding affinity, ranked? I know that we could use the command: ./vf_report.sh -c vs -d qvina02_rigid_receptor1 -n 10 to obtain the top 10 binding affinity, but I was wondering if it is possible to find the lowest 10 binding affinity, ranked

  2. After completing all the jobs, is it possible to extract which residues are interacting between the receptor and the ligand in order to understand the relationship between the two?

Thank you!

Hello eschoo and welcome to the community!

  1. For this, you can use vfvs_pp_all.sh, part of VFTools. After the full ranking of your ligands has been prepared, you can simply use something like tail to extract the last 10 (or n) number of lines from that file.
  2. Currently Virtual Flow does not incorporate such a functionality, but you could probably use something like a locally installed version of the PLIP command-line tool.

Happy docking!


vfvs_pp_all.sh is a useful script but I noticed it uses as an output only the “complete” results.
What is the difference between “complete” and “incomplete” results in output files?

Can it be used to output both “complete” and “incomplete” results like for example the following?
./vf_report.sh -c vs -d qvina_w_rigid_receptor1 -n 1000

Dear @Evangelos ,

While it might seem that the script only uses the “complete” folder, it actually uses the “incomplete” folder as well in addition automatically.

You can see this in the script “vfvs_pp_ranking_single.sh” which is called as a subscript by “vfvs_pp_ranking_all.sh”, which is called by “vfvs_pp_all.sh”.

Hope this helps,