How long do psf files take to generate?

HADDOCK
1

How long does it usually take to run? I am trying to run my first docking locally. I used to models that are known to bind for an easy first test. It has been running for a day now. Ive tried reducing the number of structures to dock down from 1000 to 1. it keeps saying waiting for the psf files, every few seconds. but its been doing that since yesterday. Is there a way I can increase the computation? I am not impatient, I want to make sure its actually working. there does not appear to be any load on the cpu at all, so I dont think much is happening.
Thank you.

2

Two possible causes:

  1. The executable you defined in run.cns is not correct

  2. There is a problem with one of your input PDB.

Did you try to run first one of the example?

Check the begin directory in your run:

  • Does it contain any files?

  • Are there generate*.out files present?

If yes, check their content, starting from the bottom of the file as this might point out to the error.

If no such files are present, then most likely there is a problem with your CNS executable

3

Thank you for your help, Professor.
Yes, i should have mentioned, I have ran haddock from within the protein-protein folder in examples, which successfully completed in basically a minute. So it is not the executable. its is something I am doing incorrectly when using the structures I want to dock, but I cannot work out where I am going wrong. I have followed your tutorial, and the best practice guide on your site, but it always ends up showing this:

[2024-05-26 20:23:13] Generating PSF and PDB file of molecule 1
chmod: untitled: No such file or directory
chmod: folder: No such file or directory
chmod: 18.35.39_run1_generate_1.job: No such file or directory
[2024-05-26 20:23:13] Generating PSF and PDB file of molecule 2
chmod: untitled: No such file or directory
chmod: folder: No such file or directory
chmod: 18.35.39_run1_generate_2.job: No such file or directory
[2024-05-26 20:23:13]   waiting for the psf files...
[2024-05-26 20:23:13]   waiting for the psf files...

and then it keeps repeating that. I tried following your tutorial, but it looks like its missing something(?)

Any ideas or places I can look? I have tried setting up a new docking with similar molecules but to no avail.

4

Most likely some errors in your run.cns…

Compare it with one from an example.

And again, what is the content of the begin directory?

5

Sorry, the begin folder contains iteration.cns,

which has

module ( iteration )
evaluate (&iteration=0)

how much should I be changing in the run.cns? in the tutorial it basically said to change histidine residues and the number of structures to be docked.

in the folder where I am running it, I have the two pdb files, the .list files for the active sites and the passive sites, and the ambig.tbl file the script produced from them. I have the run.param. The run.cns I have not edited much, as I am not very confident with all the variables.
the pdb_validate script comes clean for one molecule, and says there is an issue for the last line of the other molecule, saying 3<80, however that line is just ‘END’.

Thank you.

6

Please share your run.param and all the steps you are taking to setup a run.

The begin directory is empty (no new files created). Meaning that something is wrong in your setup.

Check carefully how the examples are setup and executed.