How to creat meta-tranches files by using the result dockingsposes which is a result file of VFVS

[chunqiongli]

Hello everyone,
After VFVS, I’ve got the top 50,000 compounds and they are They are stored in a folder called dockingsposes, but how to creat meta-tranches files by using this dockingsposes file.

Here are the two commands to get the dockingsposes file :

• head -n 50000 …/…/ranking/qvina02_rigid_site1/firstposes.all.minindex.sorted.clean > compounds

• vfvs_pp_prepare_dockingposes.sh …/…/…/output-files/complete/qvina02_rigid_site1/results/ meta_collection compounds dockingsposes overwrite

Wish eagerly to get everybody’s help!

Sincerely,
Vera

[Christoph]

Dear Vera,

I would recommend to create your custom library manually. From the paper and the VirtualFlow version of the REAL, one can see the format/hierarchy of the library on all levels.

Using commands like tar and mkdir, you could create our own custom library, which should not be difficult. You can use a single metatranche and even a single tranche, since your library is so small. That’s the way I usually do it as well when preparing smaller custom libraries for stage 2 rescreenings.

Hope this helps,
Christoph

[chunqiongli]

Yes,I have created my custom library manually. But there are some error, I have posted the detailed error message in the VFVS community

• Here are the related links:

Some errors occurred when operating the flexible docking

Dear all, Recently I’ve been using VFVS for rigid docking, and I obtained 50,000 ligands through this step. Now, I have wrote a script file to generate a Tranches file called AA from the above 50,000 ligands as the input ligands-library for my next flexible docking. But some errors occurred when operating the flexible docking, job submitted but immediately failed. I think this problem is from the input ligands-library, and I can sure that entered input receptor files are correct. I browsed all …

[dancingfish]

Hi chunqiongli:
would you like to share the method you prepare you input ligand library.
I meet some problems when performs this with my own .smi files.
I reconstruct the input files dirctory as …/input-files/AA/AABBCC/0000.tar.gz, which contains .smi files as one ligand for each file.
I run the script ./vf_start_jobline.sh ,and I crashed .
The problems report in file queue-1-1-1.out shows that

Can you share how about you reconstruct you input files .
Thank you very much!
dancingfish