How to use VFVS for flexiable docking and how to set the parameter of input-files

Dear VirtualFlow community,
I have screened out a lot of small molecules using the qvina2_rigid and smina_rigid docking program of VFVS, and now I want to continue to do the flexible docking using VFVS,but how to use VFVS for flexiable docking and how to set the parameter of input-files.Could you please help me?
Thank you very much!

Sincerely,
Vera

Hi,

You could use smina and specify flexible side chains in the config file of the chains you want to behave in dynamic manner

Hi Kaneki! Thanks for your reply, I’ll try it, but if you can give me a available template for reference, It will be a great help to me.Thank you!

The tutorial files contains a template for smina. Above the search spaca paramaters, I believe you could add --flexres arg with the chains separated by a comma which you want to be flexibile. Otherwise check the smina github

Hi kaneki, I can’t find the tutorial files contains a template for smina, but I understand what you mean, mabey I need two .pdbqt files, one is the receptor_rigid.pdbqt and other is the receptor_flexible.pdbqt. Moreover, I need add –flexres arg in the config.txt file.Is this correct?
And another problem is that can I use the dockingsposes.plain generated from the first rigid docking for the input ligand file of my next flexiable docking?
Thank you very much!

Yes add that arguman in the config txt file of smina. Make sure you set the ctrl file also to smina.

Hi kaneki,
I used dockingsposes.plain which is generated from the first rigid docking as the input-ligand file of my flexiable docking and add some flexible argument in the config txt file of smina , also set the ctrl file to smina.
But the batch job submitted immediately failed. Here are some error messages of the job.out file:
prepare-todolists.sh: line 481: [: 10000_Z2120876833_3_T1.pdb: integer expression expected

    • Warning: Could not get the length of collection 10000_Z2120876833_3_T1.pdb. Found value is: 10000_Z2120876833_3_T1.pdb. Exiting.*
      Error was trapped
      Error in bash script /var/spool/slurmd/job13362060/slurm_script
      Error on line 287
  • Trying to stop this queue and causing the jobline to fail…

Is it because the dockingsposes.plain is not ok for VFVS? What should I do?