Haddock2.2 stop in the water refine stage

Dear all,

When I ran haddock2.2 locally and in the last 20 models (I set “cpunumber” =20) in the water refine stage (totally 200 models in water refine stage), haddock seems to stop and there was not cns1 process. And I rerun haddock again and again, there is not cns1 running and 20 .out files are all empty. What can I do in this situation?

Thanks a lot for your help.

There must be something wrong in your settings for it1.
The it0 models have been generated fine, correct?
So you CNS should be fine.

If you look into the run directory, you will see job files for the it1 structures, e.g. complex_it1_refine_1.csh …

Try executing one of these manually to see if any file is generated.
Also check the content of those scripts. Probably they are writing the output files into the /tmp dir, and those are then compressed and moved back to the run dir upon completion. For this to work properly there should be also enough space in /tmp

Both it0 and it1 are OK and water refinement was stopped at last 10 structures.

I ran one of the script of the fail water refinement, and everything is OK.

But when I ran with haddock2.2 command, all of the .out files of fail water refinement are empty, even the output of the first command "echo STARTED " of script.

Can I run all of the individual .job files and then run haddock2.2 again to do the analysis step?

Thanks for your reply.

Do you see any cns process while the water refinement is running?
Check the content of you /tmp directory.

And before restarting haddock, delete any out files first

No any cns process while I used haddock2.2 command to run the water refinement.

I do the rest of the water refinement by running the .job file one by one manually and used haddock2.2 command to do the analysis.

Thanks a lot for your reply!