Good evening and sorry for the inconvenience,
I am trying to dock a protein and a metallic ligand with HADDOCK 2.4, but when I put the pdb file of both of them, I get the following error:
The following error occurred when processing one of your PDB file:
Unable to generate topology for ligand UNL. PRODRG did not create the required output: PRODRG> WARNING: more than one fragment.
Here’s a sample of the starting point of the aformentioned pdb file of my ligand:
HETATM 1 O1 UNL B 1 6.869 6.006 6.823 1.00 10.00 O
HETATM 2 O2 UNL B 1 1.467 1.378 2.882 1.00 10.00 O
HETATM 3 O3 UNL B 1 2.975 2.995 6.471 1.00 10.00 O
HETATM 4 O4 UNL B 1 1.325 6.451 7.818 1.00 10.00 O
HETATM 5 O5 UNL B 1 9.316 1.763 1.559 1.00 10.00 O
HETATM 6 O6 UNL B 1 6.463 1.306 7.799 1.00 10.00 O
HETATM 7 O7 UNL B 1 -0.223 -0.077 5.097 1.00 10.00 O
HETATM 8 O8 UNL B 1 1.366 0.812 8.028 1.00 10.00 O
HETATM 9 O9 UNL B 1 -0.503 4.516 4.170 1.00 10.00 O
HETATM 10 O10 UNL B 1 -0.337 3.967 8.678 1.00 10.00 O
HETATM 11 O11 UNL B 1 4.483 0.302 -1.140 1.00 10.00 O
HETATM 12 O12 UNL B 1 4.436 -0.694 4.362 1.00 10.00 O
HETATM 13 O13 UNL B 1 4.050 -0.344 8.860 1.00 10.00 O
HETATM 14 O14 UNL B 1 3.305 3.858 0.036 1.00 10.00 O
HETATM 15 O15 UNL B 1 4.681 4.643 8.543 1.00 10.00 O
HETATM 16 O16 UNL B 1 3.568 8.457 8.580 1.00 10.00 O
HETATM 17 O17 UNL B 1 8.747 -0.819 -0.057 1.00 10.00 O
HETATM 18 O18 UNL B 1 8.473 -0.410 4.636 1.00 10.00 O
HETATM 19 O19 UNL B 1 7.220 4.715 -0.046 1.00 10.00 O
HETATM 20 O20 UNL B 1 9.648 3.965 3.709 1.00 10.00 O
HETATM 21 O21 UNL B 1 8.460 3.547 8.611 1.00 10.00 O
HETATM 22 O22 UNL B 1 8.293 8.143 8.549 1.00 10.00 O
HETATM 23 O23 UNL B 1 4.539 4.217 4.371 1.00 10.00 O
HETATM 24 O24 UNL B 1 2.066 9.625 1.689 1.00 10.00 O
HETATM 25 O25 UNL B 1 6.541 8.128 1.695 1.00 10.00 O
HETATM 26 O26 UNL B 1 -0.268 4.542 -0.336 1.00 10.00 O
HETATM 27 O27 UNL B 1 -0.080 8.884 -0.432 1.00 10.00 O
HETATM 28 O28 UNL B 1 0.325 8.074 4.919 1.00 10.00 O
HETATM 29 O29 UNL B 1 4.322 7.904 -0.463 1.00 10.00 O
HETATM 30 O30 UNL B 1 4.226 9.813 3.918 1.00 10.00 O
HETATM 31 O31 UNL B 1 8.455 8.521 4.110 1.00 10.00 O
HETATM 32 CU1 UNL B 1 8.558 5.176 4.679 1.00 10.00 CU
HETATM 33 CU10 UNL B 1 3.686 0.794 5.267 1.00 10.00 CU
HETATM 34 CU11 UNL B 1 2.749 5.514 0.777 1.00 10.00 CU
HETATM 35 CU12 UNL B 1 8.369 0.120 1.547 1.00 10.00 CU
HETATM 36 CU13 UNL B 1 7.439 1.181 4.649 1.00 10.00 CU
HETATM 37 CU14 UNL B 1 6.591 4.234 1.679 1.00 10.00 CU
HETATM 38 CU15 UNL B 1 0.986 3.797 5.099 1.00 10.00 CU
HETATM 39 CU16 UNL B 1 4.302 3.016 1.414 1.00 10.00 CU
HETATM 40 CU17 UNL B 1 2.785 2.583 3.507 1.00 10.00 CU
HETATM 41 CU18 UNL B 1 3.345 3.319 8.271 1.00 10.00 CU
HETATM 42 CU19 UNL B 1 3.181 6.824 7.693 1.00 10.00 CU
HETATM 43 CU2 UNL B 1 1.144 1.179 4.718 1.00 10.00 CU
HETATM 44 CU20 UNL B 1 8.414 2.800 2.864 1.00 10.00 CU
HETATM 45 CU21 UNL B 1 6.795 3.175 7.778 1.00 10.00 CU
HETATM 46 CU22 UNL B 1 6.772 7.783 7.476 1.00 10.00 CU
HETATM 47 CU23 UNL B 1 5.433 5.941 2.878 1.00 10.00 CU
HETATM 48 CU24 UNL B 1 3.266 5.277 5.303 1.00 10.00 CU
HETATM 49 CU25 UNL B 1 5.443 3.172 5.669 1.00 10.00 CU
HETATM 50 CU26 UNL B 1 0.597 3.449 0.949 1.00 10.00 CU
HETATM 51 CU27 UNL B 1 1.528 8.333 0.406 1.00 10.00 CU
HETATM 52 CU28 UNL B 1 1.804 7.076 4.268 1.00 10.00 CU
HETATM 53 CU29 UNL B 1 4.771 7.534 1.342 1.00 10.00 CU
HETATM 54 CU3 UNL B 1 1.275 2.168 6.702 1.00 10.00 CU
HETATM 55 CU30 UNL B 1 4.882 8.685 5.297 1.00 10.00 CU
HETATM 56 CU31 UNL B 1 3.258 8.643 2.783 1.00 10.00 CU
HETATM 57 CU32 UNL B 1 6.783 7.823 3.554 1.00 10.00 CU
HETATM 58 CU4 UNL B 1 0.253 5.503 2.737 1.00 10.00 CU
HETATM 59 CU5 UNL B 1 1.158 4.562 7.675 1.00 10.00 CU
HETATM 60 CU6 UNL B 1 5.645 0.073 3.116 1.00 10.00 CU
HETATM 61 CU7 UNL B 1 4.570 1.111 7.763 1.00 10.00 CU
HETATM 62 CU8 UNL B 1 5.079 5.383 6.845 1.00 10.00 CU
HETATM 63 CU9 UNL B 1 4.888 0.584 0.690 1.00 10.00 CU
CONECT 1 46 62
CONECT 2 40 43
CONECT 3 41 54
CONECT 4 42 59
CONECT 5 35 44
CONECT 6 45 61
CONECT 7 43
CONECT 8 54
CONECT 9 38 58