I would like to perform covalent docking of a small molecule to a cysteine residue on my receptor. I had a look at the covalent docking tutorial, but there are some differences between re-docking a ligand based on a crystal structure and de-novo covalent docking.
Based on my limited understanding there should be some additional chemical modification to the ligand as well, in order to facilitate covalent bond formation.
Could you perhaps point me towards a tutorial that would cover such a case for HADDOCK?
But you can probably improve your docking by defining a second distance restraints to the C12 atom to enforce a better angle (if you know what the angle should be - the corresponding distance could be estimated for example from a CYS by measuring the SG - CA distance)
I am trying to resubmit the docking using the Guru interface for covalent protein-ligand docking (which worked wonderfully the previous time) but get the error message:
There was an unknown problem in the parsing of your data.
This is either a server error, or some inconsistency in your input has been detected that was not properly reported.
Please save this page from your browser as HTML and email it to firstname.lastname@example.org.
Importantly, do provide the following information:
Which interface are you accessing?
What is your access level to the HADDOCK server?
What kind of molecules are you docking?
The HADDOCK server is in constant development, thank you for your patience.
Full error information:
Traceback (most recent call last):
File “/home/enmr/services-enmr/HADDOCK2.2/py/haddockserver.py”, line 179, in serve_haddock
covproject = webform[‘covid’].value
File “/usr/lib64/python2.7/cgi.py”, line 540, in getitem
raise KeyError, key