Stuck on "waiting for the matrix file in it1/analysis" (Local installation on Ubuntu)

HADDOCK
1

Hello
I am running HADDOCK2.2 on Ubuntu 15.04 (local installation).
After a while, the algorithm seems to get stuck on this part: “waiting for the matrix file in it1/analysis”

Prior to this, the following awk errors occurred:

“awk: count_hbonds.awk: line 53: syntax error at or near *”

*.out files in …/it1/analysis include:
print_dih
print_dist_all
print_dist_hbonds
print_dist_noes
print_noe
print_noe_all
print_noe_ambig
print_noe_unambig

Plus the following *out.gz
edesolv
ene-residue
energy
fcc
print_dani
print_geom
print_hbonds
print_nb
print_noes
print_rg
print_sani
print_vean
print_xpcs
print_xrdc.

Additionally, the following DONE files are also present:

DIH_DONE
DONE
ENE_DONE
HBONDS_DONE
NB_DONE
NOE_DONE

Am I missing something?

Any help would be greatly appreciated.

Best regards
Rui Almeida.

2

Did you compile the analysis programs coming with HADDOCK?
I.e. did you run make in the main HADDOCK install dir?

Also which clustering method are you using? FCC or RMSD?

Calculating the RMSD matrix can take a few hours depending on the size of your system and number of models. FCC should be much faster.

If you want it to proceed, a simple solution would be to create the MTX_DONE file in the it1/analysis directory (assuming you are running HADDOCK2.2):

touch structure/it1/analysis/MTX_DONE

This should make HADDOCK continue, but won’t fix the clustering issue.

3

Dear Alexandre
I had indeed run make in the haddock installation directory.
Creating MTX_DONE solved the issue.

Thank you for your help.
Rui A.