Hi,
Sometimes when I perform docking, the results seem illogical.
For instance, the bond length exceeds 10 Å, which doesn’t make sense.
What could be causing this?
Thanks!
Strange - does this only happen at a Pro-Pro connection?
Can you share a link to the run if you used the server?
I didn’t use the surver
I so far I only noticed this on Proline-proline
Which haddock version are you using?
And can you share your input PDB file for the peptide?
Thank you
haddock2.4
I have 30 input files (for the peptide) but I can only upload 5.
I noticed that also in some of the begin file the length is too large(even when it’s just Proline alone and not Pro-Pro)
frame_840.pdb (11.4 KB)
frame_993.pdb (11.4 KB)
frame_1004.pdb (11.4 KB)
frame_724.pdb (11.4 KB)
frame_754.pdb (11.4 KB)
Hi,
Do you have any ideas? Can I maybe email you all the files?
Thank you very much
There is something fishy with your PDB files.
From the 5 you shared 993 gives a problem.
After running it through our pdb-tools pdb_tidy it runs fine.
I suggest you process all you PDBs first with pdb_tidy
Thank you very much
I did your suggestion, but I am still getting the same error.
Is it possible to send you the file run?
Yes - send me a direct email with a link to download it (also the input data in that case).
PS: I tested your system with haddock2.5