Chemical molecule PDB format issue for haddock input

HADDOCK
1

Dear All,

I converted the smi file of chemical structure into pdb file as the haddock input. However, I got this error warn “Error in PDB file. Your PDB contains multiple residues with number 1 in chain A or duplicated atom names”. I would like to know how to fix it (e.g. command line from pdb-tools or other tools). Thank you!

###########################pdb file############################
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.90
HETATM 1 C UNL 1 0.358 2.855 0.092 1.00 0.00 C
HETATM 2 C UNL 1 0.075 1.764 -0.740 1.00 0.00 C
HETATM 3 C UNL 1 0.736 0.550 -0.578 1.00 0.00 C
HETATM 4 C UNL 1 1.702 0.377 0.428 1.00 0.00 C
HETATM 5 C UNL 1 1.326 2.713 1.126 1.00 0.00 C
HETATM 6 C UNL 1 1.982 1.472 1.274 1.00 0.00 C
HETATM 7 H UNL 1 0.484 -0.259 -1.252 1.00 0.00 H
HETATM 8 C UNL 1 -0.378 4.132 -0.175 1.00 0.00 C
HETATM 9 H UNL 1 -0.659 1.860 -1.531 1.00 0.00 H
HETATM 10 C UNL 1 1.670 3.815 2.080 1.00 0.00 C
HETATM 11 H UNL 1 2.712 1.382 2.059 1.00 0.00 H
HETATM 12 C UNL 1 2.392 -0.953 0.552 1.00 0.00 C
HETATM 13 C UNL 1 -1.855 4.161 0.209 1.00 0.00 C
HETATM 14 C UNL 1 0.314 5.176 -0.758 1.00 0.00 C
HETATM 15 C UNL 1 -0.301 6.497 -1.088 1.00 0.00 C
HETATM 16 C UNL 1 -2.694 5.279 0.009 1.00 0.00 C
HETATM 17 SI UNL 1 -2.062 6.811 -0.737 1.00 0.00 Si
HETATM 18 C UNL 1 0.410 7.491 -1.656 1.00 0.00 C
HETATM 19 C UNL 1 1.763 5.024 -1.120 1.00 0.00 C
HETATM 20 C UNL 1 1.858 7.337 -1.998 1.00 0.00 C
HETATM 21 C UNL 1 2.470 6.011 -1.685 1.00 0.00 C
HETATM 22 N UNL 1 2.552 8.309 -2.549 1.00 0.00 N
HETATM 23 H UNL 1 2.295 4.097 -0.939 1.00 0.00 H
HETATM 24 H UNL 1 3.511 5.803 -1.908 1.00 0.00 H
…
HETATM 85 H UNL 1 -0.707 -6.680 3.807 1.00 0.00 H
HETATM 86 H UNL 1 -1.010 -8.135 2.975 1.00 0.00 H
CONECT 1 2 5 8
CONECT 2 1 3 9
CONECT 3 2 4 7
CONECT 4 3 6 12
CONECT 5 1 6 10
CONECT 6 5 4 11
CONECT 7 3
CONECT 8 1 13 14
CONECT 9 2
CONECT 10 5 58 59
CONECT 11 6
CONECT 12 4 61 62
CONECT 13 8 16 26
CONECT 14 8 15 19
CONECT 15 14 17 18
CONECT 16 13 17 27
CONECT 17 15 16 34 35
CONECT 18 15 20 25
CONECT 19 14 21 23
CONECT 20 18 21 22
CONECT 21 19 20 24
CONECT 22 20 42 46
CONECT 23 19
…
CONECT 86 83
MASTER 0 0 0 0 0 0 0 0 86 0 86 0
END

###########################pdb file############################

2

Atom names must be unique

Check for some instruction on generating ligand conformations our most recent shape-restrained docking tutorial

https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/#3b-generating-an-ensemble-of-conformations-for-the-ligand-to-be-docked

1 Like
3

Thank you, amjj. Your answer fully addressed my issue.