HADDOCK failed in the clustering of the solutions

HADDOCK
1

Dear all,
It seems that my run on the web completed successfully, but there was an error in the clustering of the solutions.
I do not know how to correct the error. I report here the last rows written on the file named haddock.out:

file.list exists => iteration 0 finished.
looking for iteration 1
file.list exists => iteration 1 finished.
CNS analysis files in it1/analysis already exist.
To rerun the analysis delete the “DONE” file in the analysis directory.
file it1/water/file.list already exists => water refinement done.
CNS analysis files of the water refined structures already exist.
To rerun the analysis delete the “DONE” file in the analysis directory.
Cluster file in it1/analysis already exist.
To rerun the clustering delete the “CLUST_DONE” file in the analysis directory.
waiting for the ene-residue file in it1/analysis…
ene-residue file in it1/analysis is found
Cluster file in it1/water/analysis already exist.
To rerun the clustering delete the “CLUST_DONE” file in the analysis directory.
waiting for the ene-residue file in it1/water/analysis…
ene-residue file in it1/water/analysis is found
Now compressing the output files…
Cleaning up the run directory …
##############################################################################
Finishing HADDOCK on: 2016-11-28 10:59:45
Au revoir.
Tot ziens.
Bye bye.
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…
chmod: changing permissions of /home/enmr/services-enmr/HADDOCK2.2/server/results/8349133175/hcn2tripnov17B': Operation not permitted chmod: changing permissions of/home/enmr/services-enmr/HADDOCK2.2/server/results/8349133175/hcn2tripnov17B/index.html’: Operation not permitted
chmod: changing permissions of `/home/enmr/services-enmr/HADDOCK2.2/server/results/8349133175/hcn2tripnov17B/haddockparam.web’: Operation not permitted

There is a way to run the last part of the program without starting from the beginning? Can I run it locally starting from the clustering?

thanks a lot Francesca

2

Hi Francesca

Download the tar archive and perform a local analysis. You can try various cutoffs and see if clustering will work or now.

See http://www.bonvinlab.org/software/haddock2.2/analysis/#manual

And depending on the option selected in run.cns (RMSD or FCC clustering) try a manual clustering using various cutoffs.

3

thanks a lot
Francesca

4

For peptide-protein complex it is better always decrease the RMSD to 5 or 2,5 A . Is it ok?

I have followed a protocol reported in the article: Plos One 2013 Trellet, Melquiond Bonvin
where all the residues of the peptide are included as passive. I have also introduced them as fully flexible and increase tha MD steps as described in the article.Could be this the reason why the program stopped ?

I have noticed that if I use only one structure for the protein and for the peptide the output is much much better than when I use a family of 10 conformers for the peptide.
Thanks
Francesca

5

Hello Francesca,

You’re referring to the error message you mentioned in the 1st post I guess? This protocol has been used for many cases and should not trigger this error, seems quite independent from the protocol but more an issue on the server. We’ll try to investigate the probem.

Are the results on which you based your observation coming from successful HADDOCK runs using the web server?
By “much much better”, do you have a reference structure to compare with or is it an overall look of the HADDOCK models that makes you say that results are better? It is hard to draw an explanation out of the few information we have but I’ll be happy to help you understand the reason of such difference providing a bit more explanation of what are the input data.

Looking forward to hear from you,

Best,

Mikael Trellet

6

Regarding the “stopped” program, what do you mean exactly?
Many reasons for this are possible. Simply stop the haddock python process, delete any *.out file in the run dir and restart.