Problem with Analysis in Local HADDOCK set-up

HADDOCK
1

Hello Everyone,

I am new to HADDOCK and am trying to use it for protein-protein docking with PCS values. Initially the run seems to work well, however when it moves onto the cluster analysis step i get the following error message: waiting for “matrix/it1/analysis” , and the run stalls. All of the models for the it0, it1, and water steps are generated, but a majority of the analysis steps - ranging from RMSD calculations, pcs error output etc., never completes.

Has anyone ever encountered this error?

2

What is the content of the analysis directory?

There might be several reasons why it is pending, e.g.:

  • a problem with the it1 models
  • problems with the haddock installation
  • …
3

Hello,

The analysis directory contains:

  1. fitted pdb files for the models generated
  2. the reduced coordinates file (which puts the PCS energy at 0)
  3. the fcc.out.gz file (which when opened states “python: No match”
  4. the get_average.out.gz file
  5. the iteration.cns file (which when opened is comprised of two lines stating module (iteration 1) and evaluate (&iteration1)
  6. the rmsave.disp file
  7. the rmsdseq.disp file

Thank you.

4

Point 3 below is your problem

  1. the fcc.out.gz file (which when opened states “python: No match”

There must be a problem with the python version used to run the contact analysis / clustering.
It does required python2.7

In the run dir you should see a …fcc…job file.
Try executing manually. If working there should be .contacts files appearing in the analysis directory.

Also check that the contact_fcc executable is present in the tools directory (should have been compiled when you installed haddock2.4)