Dear Dr. Bonvin,
Hi,I am a new user of haddock. I deployed haddock locally and recompiled CNS. However, when running the examples, the log file outputs the following information: waiting for the psf files…
Error in the topology generation: prot_psf_mol1 could not be created. So I don’t know what the reason for this problem is now? Because I have indeed recompiled CNS.
Most likely an issue with your CNS executable, or the wrong path to the CNS exec is given in the run.cns file.
Did you try one of the executable provided in the email about the HADDOCK distribution?
Dear Dr. Bonvin,
Thank you very much.I have solved this problem. The reason is that I did not replace the bin, lib, and source files in the cns directory you distributed when compiling cns. I mistakenly thought that recompiling meant copying the entire cns directory. In fact, recompiling means that the compiler will look for files in these three directories in the directory instead of scanning other directories.
Dear Dr. Bonvin,
Thank you very much. I have another question for you. When I was preparing to dock my two proteins’ pdb data, I put my two pdb data under protein-protein under example, and then modified the parameters. According to the prompts on the official website, I modified the following parameters (the parameters with decimals were not changed). Because I did not set any constraints here, I would like to ask you how to perform unconstrained protein-protein molecular docking prediction in local deployment? The final result is that there is no docking result, and the proteins are far apart. I would be very grateful if you can help me.
Check out best practice guide and in particular the ab-initio section.
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How to use information about interactions in HADDOCK? |
In your case the centre-of-mass restraint option would be the best
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HADDOCK2.4 manual - Ambiguous Interaction Restraints (AIRs) |
Dear Dr. Bonvin,
Thank you very much, I will try the next experiment according to your help.Thanks again for your help
Dear Dr. Bonvin,
Sorry to bother you again. After listening to your advice, I set the center of mass constraint to true, that is, cmrest=true. Then I ran my example. The result this time was better than the last time, because I found that the distance between proteins became much smaller. However, I also found a new problem. The final docking result will change the conformation of the secondary structure of one of my proteins. The following is the structure of the protein before docking.
This seems to have changed the conformation of my original secondary structure, so that this is the final docking result. The blue one on the right is the protein, and it seems to have changed its previous conformation.I hope to get your help again, I will be very grateful.
this is very strange.
did you change any other parameters?
My guess is that there is an issue already at the topo generation stage pointing to a problem with your input PDB. Can you check the PDB files to n the begin directory? Or one random file from structures/it0
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Dear Dr. Bonvin,
I only modified the parameters for the number of structures in the it0, it1, and water stages, and set the centroid restraint to true (i.e., cmrest=true). However, when I later checked the entire series of 7fbk protein PDB files in the begin directory and visualized them with PyMOL, I found that only one was correct while the other conformations were not quite right. This ultimately led to problems with the docking conformations. The following images show, respectively, the structure PDB files in my begin directory, the corresponding visualizations of these PDBs, and finally the docking conformations.And the last screenshot of the parameters I modified.
![0e42d97d1d1a1f11ba364c37ee7296a|690x285]
Most likely an issue with chainID/segID in your ensemble for input PDB files. Check the files in the examples/protein-protein directory. You might have to remove all chainIDs
Dear Dr. Bonvin,
Thank you thank you.