I have given all the necessary details for docking study in the Haddock webserver (https://milou.science.uu.nl/services/HADDOCK2.2/haddockserver-easy.html) with correct username and password at the end of the page. But, the server says “There was an error in the authorization routine of the server, Incorrect password for the username”. But, the username and password are correct. To confirm this I have created an another account with different email id, but still the server says incorrect password. Please, help in this regard. Thank you.
Sorry for the delay, could you finally launch a HADDOCK run? To check if your username (or email) / password combination is ok, please log in on https://nestor.science.uu.nl/usr
If you can log in there is no reason the authentication fails upon job submission. If this is still the case we will investigate further. Keep us in touch,
Thanks for your reply. My account has been activated now.
I am doing DNA-protein docking. But, I got error during analysis. I got the active and passive restraints from CPORT for the protein. But, i could not get restraints for the DNA molecule. Can you help with this. Thanks.
There was an error in rigid body stage of the docking.
TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!
CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS
STRUCTURE NUMBER 1
You must define restraints between the two molecules, not only on the protein side, otherwise the first docking stage (rigid body) will fail and return such an error. Do you have any idea where the protein binds? Major or minor groove? Some specific DNA sequence? etc …
If you do not have any clue about the DNA binding, you can specify the whole DNA sequence as passive. This remains suboptimal regarding HADDOCK’s philosophy but it would fix your error.
Another remark, you probably can make some educated guess on the protein side for the putative DNA binding site (positively charged patch of residues at the surface, exposed arginine(s), conserved residues), and refine CPORT predictions.