Hi, I am completely new to this. I have submitted a docked complex obtained from Cluspro to Haddock but the run failed. I noticed they mentioned “structure contains gaps” but I have not edited the protein structures so it should be from the original pdb files. Can you kindly suggest how should I fix this issue?
Thank you in advance!
Dear Ashley,
Looking at your log file:
Structure contains gap, is just a warning, and you should not worry about it !No contacts found for selection. This means the two chains are not in contact, therefore binding affinity prediction with Prodigy cannot be computed, as there is no binding between the two partners.Have you looked at your submitted complex on a molecular visualizer (e.g:PyMOL) ?
Cheers
Dear Victor,
Thank you for replying! I have checked the docked complex on Pymol and their energy score is -1091 so technically they should be interacting. I have included the Pymol view below.
But are the chain names correct? You specified A and B
Hi,
Yes, I made sure I categorized the respective proteins into Chain A and B by using the type alter (sele), chain=’A/B’ command in Pymol.
Could you send me your pdb file so I can investigate ?
Sure, how should I send it to you? Maybe you can share your email as I cannot send attachments as a new user.
Hi all,
I attempted once more, this time I removed the chains that were not interacting based on what I saw on Pymol and it went through. I’m wondering if this is the right way? Was this error due to the complex being too large?
Good to know you managed !
I would rather go for a miss selection of the chains to be analyzed by Prodigy.
It is weird.
Here is my email (v.g.p.reys@uu.nl) if you want to send me the full original structure for us to know where the problem comes from
