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

VFVS VFVS 1
#1

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

#2

Hi,

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

#3

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!

#4

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

#5

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!

#6

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

#7

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?