Hello!
I need run a docking calculation using as receptor a protein-fat acid complex and DNA as ligand, but the HADDOCK gives me an error: “The following error occurred when processing one of your PDB file: Unable to generate topology for ligand PLM. PRODRG did not create the required output: PRODRG> Molecule complexity index: 1.89”.
Can You help me? Im new in this software.
Is this my pdb in ligand section:
…
ATOM 2542 HA ASP A 168 87.171 77.106 55.559 1.00 13.33 H
ATOM 2543 HB1 ASP A 168 84.341 76.401 55.085 1.00 13.33 H
ATOM 2544 HB2 ASP A 168 85.557 75.754 53.962 1.00 13.33 H
TER 2545 ASP A 168
HETATM 2546 C1 PLM A 169 68.039 59.498 74.653 -0.09 0.00 .000 C
HETATM 2547 C2 PLM A 169 67.403 60.417 75.702 -0.09 0.00 .000 C
HETATM 2548 C3 PLM A 169 67.808 61.891 75.775 -0.14 0.00 .000 C
HETATM 2549 C4 PLM A 169 68.099 59.937 73.186 -0.21 0.00 .000 C
HETATM 2550 C5 PLM A 169 66.827 60.416 72.478 -0.21 0.00 .000 C
HETATM 2551 C6 PLM A 169 65.647 60.994 71.691 -0.29 0.00 .000 C
HETATM 2552 C7 PLM A 169 65.506 60.712 70.191 -0.29 0.00 .000 C
HETATM 2553 C8 PLM A 169 64.087 60.910 69.650 -0.38 0.00 .000 C
HETATM 2554 C9 PLM A 169 64.299 62.387 69.346 -0.30 0.00 .000 C
HETATM 2555 C10 PLM A 169 64.299 63.520 70.377 -0.34 0.00 .000 C
HETATM 2556 C11 PLM A 169 68.880 62.343 76.773 -0.08 0.00 .001 C
HETATM 2557 C12 PLM A 169 64.712 64.936 69.958 -0.52 0.00 .005 C
HETATM 2558 C13 PLM A 169 64.804 65.832 71.206 -0.42 0.00 .005 C
HETATM 2559 C14 PLM A 169 68.481 63.158 78.008 -0.14 0.00 .010 C
HETATM 2560 C15 PLM A 169 67.564 64.375 77.860 -0.19 0.02 .110 C
HETATM 2561 C16 PLM A 169 67.303 65.289 79.061 -0.18 0.11 .139 C
HETATM 2562 O17 PLM A 169 67.319 64.829 80.195 -0.03 -0.71 .650 O
HETATM 2563 O18 PLM A 169 67.053 66.608 78.868 -0.44 -0.80 .776 O
END
Thanks!!!