The backbone rmsd matrix was not calculated by HADDOCK (locally installed)

HADDOCK
1

Dear All

I was able to run Haddock2.2 locally following the web tutorial (but using my system as input), previously I edited run.cns in haddock web server, and then run in a linux terminal: haddock2.2

After 18 hs of work the script had stopped writing in the terminal and there was no evidence of cpu work, but it did not gave me the shell prompt back, so I supposed that It has not finished. Anyway I stopped it manually because I did not know what to do.
I found inside run1 directory: the structures of it0 and it1, with some analysis done, but not the backbone rmsd matrix calculations. So, I could obtain and see the ene_rmsd.xmgr, but not the next analysis described in:

http://www.bonvinlab.org/software/haddock2.2/tut_e2a-hpr-csp/#analysis

  1. Is it possible to run rmsd.inp after I stopped Haddock2.2 run?
  2. Suppose that Haddock run is stopped before it has finished (for example, due to a power cut, which is quite common in our city). Is it possible to re-run the haddock without loosing what it is already done?

Thank you very much in advance!!

2

You can always restart a HADDOCK run when stopped.

As for the rmsd matrix, it depends if you defined RMSD or FCC in run.cns (the default is FCC now). FCC stands for fraction of native contacts.

Did you compile the utilities when installing HADDOCK? I.e. did you give a “make” command in the install dir?
It could be the run completed fine but is waiting for clustering output - which might fail if the program was not compiled.
Go also into the tools dir of your current run and type make, then restart HADDOCK

3

Thank you Dr. Bonvin for your fast answer!

I had compiled Haddock tools before running the docking, but as you said run.cns was set to use FCC option. If I change the analysis option in run.cns and run haddock2.2 again, it will calculate the backbone rmsd matrix?

4

To be sure empty first the analysis directories.

Also this matrix is not what is used to generate the ene_rmsd.xmgr files mentioned in the tutorial.
Rather a post analysis calculating RMSDs from the known reference structure.