I have a pdb file with a ligand and a protein linked covalently. It is a cysteine residue. I know that to run a covalent docking this bond is needed. However, when I import the pdb to GOLD software this bond is broken, and I do not know how to prepare both the ligand and the protein in order to run the covalent docking.
Does anyone know how to manipulate this entities so they can work in covalent docking?
please follow that tutorial about preparing the covalent link from available options given on the left of the GOLD Setup window
http://scbx.mssm.edu/mezeilab/molmod/gold_docs/gold.1.61.html#291952
http://scbx.mssm.edu/mezeilab/molmod/gold_docs/gold.1.284.html
I have tried this method Mohammad Tarek. However, to run this method you should have a pdb file that both the protein and the ligand have a common atom (they are covalently bonding). Although my pdb file has this feature, when I import the file to the Gold software, the software breaks the covalent bond between the protein and the ligand and I cannot run the covalent docking.
I was wondering how to fix this (How I can import the pdb file with no bond cleavage).
It should works, So would you check your file, may be there is something worng with the bond parameters, you may use Avogadro for that
https://avogadro.cc/
@Mohammad, I had indeed to manipulate the files. What I did was adding the same sulfur atom to the ligand. By doing that I could set the covalent bond between the sulfur of the protein and the sulfur of the ligand.
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