PCS restraints - 0 violations shown in print output

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

I am using the web interface for PCS ligand docking but the output files are giving no violations (even when i input completely false data).

  1. How can I confirm that the PCS data are being implemented correctly and in which iterations?
  2. How can I alter the output so it gives useful PCS violation statistics?
  3. Can I change the print limits for violation outputs and if so, how?
2

To which output files to do you refer?

And did you follow the instructions to properly define the PCS restraints? E.g.

      http://www.bonvinlab.org/software/haddock2.2/PCS_help/

Here is an example run with PCS restraints (you can download the full tar archive):

     https://milou.science.uu.nl/serviceresults/HADDOCK2.2/1111111111/test-PCS/

To know if you restraints were successfully read, you should download the full run and look in the run directory into the various out files (e.g. the one from it0) and search for error messages. The section reading the restraints will have the following string: XDIPO_PCS>

And in the analysis directory structures/it1/water/analysis you should find a xpcs.disp file that lists the number of violations per complex

3

Thanks very much.

Is there a similar test set with a ligand instead of two proteins so I can check the pdb and pcs file formattiing?

4

No - but the PCS file formatting will not change, only the atom names and residue numbers. Make sure to define the restraints to existing ligand atoms (I recommend here to use heavy atoms).

5

Using the run file, I have ascertained that the pcs file cannot call the pdb file atom, meaning there is a problem with one or other.

I have used the test pcs file and replaced the atom names and pcs values directly with mine and that still didn’t work.

Comparing the pdb files for the protein and ligand, the only differences are the additional column with C H N F etc in and the CONNECT lines at the bottom of the ligand file and Model 1 at the top of the prot file.

I have checked that I am using HETATM instead of ATOM, that all atom names are different and that the columns are the same as those in the protein pdb file (which is being called correctly for the pcs restraints)

Any other suggestions I should check?

6

Define “that still didn’t work”

Do you see error messages in your output files that your restraints have not been read properly? I.e. no atom selected?

And otherwise email me a PDB file (e.g. from the begin dir), your restraint file and an example output file