Hello
I have a protein with the palmitic group on ser212 as a receptor and I want to dock protein as a ligand with it. I docked it with haddock but the result indicated displacement of the palmitic acid so I want to put the restrain on it. unfortuently I do not know how to make a TBL file. could you send me a protocol on how to make this file and help me in this field?
thanks
The format of the restraints follows CNS/Xplor syntax. You can find various examples in our online tutorials at bonvinlab.org/education
It is also explained in Box4 of our Nature Protocol paper describing the HADDOCK server.
Further ourvhaddock-tools repo on GitHub contains a Python script called restrain_ligand.py that will generate automatically a few restraints to keep a ligand in place.
Check: https://github.com/haddocking/haddock-tools
The repo also contains quite a number of handy scripts. Check it out!
thanks so much for your answer. I made a TBL file with haddock tools but gain a little bit of distance(between Se212 and PAM) was observed between ligand and receptor after ducking. how can I solve this problem?
I will send you my receptor PDB file, docking result of my complex, and TBL file
I really appreciate if you helping me in this field. cluster1_1.pdb (446.3 KB)
hwnt3a_PAM.tbl (268 Bytes) hwnt3a.pdb (201.3 KB)
You probably can’t solve the problem. Since the ligand is not covalently bound in the docking, the van der Waals interactions will effectively push it back a bit.
You could try however to replace the SER to which is it attached by CYC, which is a modified CYS, without hydrogen on the sulfur and reduced van der Waals parameters on the sulfur.
This will allow shorter distances.
And if the solutions look reasonable, simply change it back to a SER, renaming the sulfur atom to an oxygen.
in receptor crystallography pdb file (wnt3a.pdb) C1 of Palmitic acid covalantly attach to OG1 of Ser212 and I used this pdb file for generating TBL file so what is my fault for making TBL file?