Ligand PDB error


#1

Dear Dr. Bonvin and Haddock team

“Q!!n” on protein ligand docking sing CSP data in guru interface.

I have created my ligand pdb similar to Rifampicin.pdb (format available bellow)
But I’m getting error saying “Second pdb (ligand) file contains multiple residues with number 1300 in chain B”?
My ligand coordinates have 4 column(zero zero) would it be causing this issue?

Any help I would highly appreciate…
With many thanks
Vince

=====================PDB format comparison=================
#1300
HETATM23323 N3 LIG B1300 1.519 5.707 -2.767 0.00 0.00 N
HETATM23324 N4 LIG B1300 3.112 -0.838 0.324 0.00 0.00 N
HETATM23325 C1 LIG B1300 2.147 0.067 -0.060 0.00 0.00 C
HETATM23326 C2 LIG B1300 2.697 1.363 -0.642 0.00 0.00 C
END

#rifampicin
HETATM23359 C1 RFP C2002 -65.130 -23.409 -65.099 1.00135.37 C
HETATM23360 C2 RFP C2002 -65.076 -23.965 -66.364 1.00135.36 C
HETATM23361 C3 RFP C2002 -66.125 -23.790 -67.258 1.00135.72 C
END


#2

Is this your entire ligand? There must be two atoms with the same name and same residue number.


#3

Dear Dr. Bonvin and Haddock team,

Thank you, with your suggestion problem is been addressed.
Again, with many thanks
Vince


#4

Dear Sir, I am also facing the same problem could you please tell me what is wrong with my pdb file.

. I use chemdraw to draw mol files then open them in MacBook text editor, copy and paste it in open babel and then convert it to pdb or use mol2 files and convert it to pdb using open babel.


#5

All your carbons have the same name, same with hydrogens, etc. You have to make them unique. If you load the ligand in Pymol and type ‘rename’ and then save the PDB this should work.


#6

And to add to that, ligands must use HETATM instead of ATOM in the PDB file to be accepted by HADDOCK