Is it normal for flexible docking to take up a lot of inodes in /tmp?

VFVS VFVS 1
#1

Hi everyone,
Recently I have launched a flexible docking using VFVS. 50000 ligands were used and 20 amino acid residues at the binding site were set to be flexible. Docking_scenario_programs was vina. The job which was submited works fine, but there are a lot of small files in the /tmp directory that use a lot of inodes. So I have a problem, is this normal? Is there any parameter setting error?

Sincerely,
Vera

#2

Hi Very,

There should be quite some small files, but not too many for the file system to handle. Roughly how many are you referring to?

By this chance, if you use 20 flexible residues, then AutoDock Vina might not work well anymore. Instead I would recommend GWOVina or ADFR. ADFR was already supported by VFVS, support for GWOVina we have added recently:

Best,
Christoph

#3

Hi Dr Christoph，
Thank you for your reply. I have solved this problem which is about generating a lot of small files. The reason is that a lot of other files were saved in the ligand-library folder with my target ligands(fourth hierarchical level).Thank you for sharing this article.
:grin:
Best wishes,
Vera

1 Like
#4

Dear Vera,

Great, I’m happy that you were able to solve the problem :blush:

Happy holidays,
Christoph