Hello,
I am currently trying to use HADDOCK2.4’s webserver to run a covalent docking scenario. The idea is to use NO as a ligand to test if an s-nitrosilation of a cysteine residue is possible. However, I am running into this error ‘Unable to generate topology for ligand NO. PRODRG did not create the required output: ’ when using the pdb file I’ve attached below for the ligand.’ Is there any fix to this issue by editing the pdb? Is it due to the minuscule size of the ligand?
At the moment I am following the procedure shown on this tutorial: Modelling a covalent inhibitor of cathepsin proteins – Bonvin Lab
Also, there are topology files available in the ATB server (Prodrg is discontinued it seems) yet I don’t know how add them on HADDOCK’s webserver.
This is the pdb file:
HEADER NO
HETATM 1 N NO 0 -0.075 0.000 0.608 0.00 0.00 N
HETATM 2 O NO 0 0.020 0.000 -0.605 0.00 0.00 O
CONECT 1 2
CONECT 2 1
END
PD.: I am using the webserver since the laptops we have available at the moment lack the resources to run a local version of haddock in a reasonable amount of time.
Thank you.