Problem with ligand with same atoms

HADDOCK
1

I want to make a protein-ligand docking. The protein I am using has another ligand that corresponds to a polyisoprene (10 repeats) that has the following PDB structure:
HETATM 5760 C cis 379 34.381 55.304 40.093 0.00 0.00 0|** C
HETATM 5761 C cis 379 34.996 55.924 38.972 0.00 0.00 0|** C
HETATM 5762 C cis 379 35.016 57.342 38.866 0.00 0.00 0|** C
HETATM 5763 C cis 379 34.420 58.139 39.881 0.00 0.00 0|** C
HETATM 5764 C cis 379 35.592 55.127 37.958 0.00 0.00 0|** C
HETATM 5765 C cis 379 34.978 59.404 40.211 0.00 0.00 0|** C
HETATM 5766 C cis 379 34.382 60.201 41.226 0.00 0.00 0|** C
HETATM 5767 C cis 379 33.456 61.221 40.877 0.00 0.00 0|** C
HETATM 5768 C cis 379 34.712 59.978 42.590 0.00 0.00 0|** C
HETATM 5769 C cis 379 35.638 58.957 42.938 0.00 0.00 0|** C
HETATM 5770 C cis 379 35.404 58.145 44.082 0.00 0.00 0|** C
HETATM 5771 C cis 379 34.527 57.029 43.993 0.00 0.00 0|** C
HETATM 5772 C cis 379 33.188 57.139 44.456 0.00 0.00 0|** C
HETATM 5773 C cis 379 34.990 55.803 43.441 0.00 0.00 0|** C
HETATM 5774 C cis 379 36.330 55.694 42.978 0.00 0.00 0|** C
HETATM 5775 C cis 379 36.675 54.688 42.036 0.00 0.00 0|** C
HETATM 5776 C cis 379 38.007 54.193 41.981 0.00 0.00 0|** C
HETATM 5777 C cis 379 38.798 54.410 40.821 0.00 0.00 0|** C
HETATM 5778 C cis 379 38.548 53.482 43.088 0.00 0.00 0|** C
HETATM 5779 C cis 379 37.756 53.266 44.248 0.00 0.00 0|** C
HETATM 5780 C cis 379 37.347 51.949 44.594 0.00 0.00 0|** C
HETATM 5781 C cis 379 36.555 51.732 45.755 0.00 0.00 0|** C
HETATM 5782 C cis 379 35.875 50.497 45.931 0.00 0.00 0|** C
HETATM 5783 C cis 379 36.443 52.751 46.739 0.00 0.00 0|** C
HETATM 5784 C cis 379 35.986 49.478 44.946 0.00 0.00 0|** C
HETATM 5785 C cis 379 34.921 49.253 44.032 0.00 0.00 0|** C
HETATM 5786 C cis 379 33.869 48.360 44.372 0.00 0.00 0|** C
HETATM 5787 C cis 379 34.113 46.960 44.418 0.00 0.00 0|** C
HETATM 5788 C cis 379 32.574 48.865 44.666 0.00 0.00 0|** C
HETATM 5789 C cis 379 35.409 46.454 44.124 0.00 0.00 0|** C
HETATM 5790 C cis 379 36.139 46.968 43.019 0.00 0.00 0|** C
HETATM 5791 C cis 379 37.435 46.461 42.726 0.00 0.00 0|** C
HETATM 5792 C cis 379 37.575 45.244 42.004 0.00 0.00 0|** C
HETATM 5793 C cis 379 38.589 47.171 43.153 0.00 0.00 0|** C
HETATM 5794 C cis 379 36.419 44.534 41.577 0.00 0.00 0|** C
HETATM 5795 C cis 379 36.541 43.485 40.627 0.00 0.00 0|** C
HETATM 5796 C cis 379 35.510 42.513 40.503 0.00 0.00 0|** C
HETATM 5797 C cis 379 35.839 41.132 40.439 0.00 0.00 0|** C
HETATM 5798 C cis 379 34.151 42.924 40.445 0.00 0.00 0|** C
HETATM 5799 C cis 379 37.296 40.692 40.502 0.00 0.00 0|** C
HETATM 5800 C cis 379 37.703 39.327 39.965 0.00 0.00 0|** C
HETATM 5801 C cis 379 38.115 39.174 38.506 0.00 0.00 0|** C
HETATM 5802 C cis 379 39.459 39.713 38.034 0.00 0.00 0|** C
HETATM 5803 C cis 379 40.391 40.404 39.020 0.00 0.00 0|** C
HETATM 5804 C cis 379 41.649 39.694 39.505 0.00 0.00 0|** C
HETATM 5805 C cis 379 42.581 40.386 40.491 0.00 0.00 0|** C
HETATM 5806 C cis 379 43.888 40.998 40.003 0.00 0.00 0|** C
HETATM 5807 C cis 379 44.262 40.918 38.529 0.00 0.00 0|** C
HETATM 5808 C cis 379 37.183 38.483 37.520 0.00 0.00 0|** C
HETATM 5809 C cis 379 42.207 40.465 41.965 0.00 0.00 0|** C
HETATM 5810 H cis 379 34.465 54.198 39.999 0.00 0.00 0|** H
HETATM 5811 H cis 379 34.889 55.636 41.026 0.00 0.00 0|** H
HETATM 5812 H cis 379 33.306 55.591 40.132 0.00 0.00 0|** H
HETATM 5813 H cis 379 35.492 57.822 37.998 0.00 0.00 0|** H
HETATM 5814 H cis 379 33.368 58.324 39.568 0.00 0.00 0|** H
HETATM 5815 H cis 379 34.581 57.539 40.805 0.00 0.00 0|** H
HETATM 5816 H cis 379 35.477 54.050 38.215 0.00 0.00 0|** H
HETATM 5817 H cis 379 35.091 55.331 36.985 0.00 0.00 0|** H
HETATM 5818 H cis 379 36.674 55.376 37.878 0.00 0.00 0|** H
HETATM 5819 H cis 379 36.030 59.219 40.524 0.00 0.00 0|** H
HETATM 5820 H cis 379 34.817 60.004 39.287 0.00 0.00 0|** H
HETATM 5821 H cis 379 33.327 61.243 39.772 0.00 0.00 0|** H
HETATM 5822 H cis 379 32.475 61.012 41.360 0.00 0.00 0|** H
HETATM 5823 H cis 379 33.840 62.206 41.225 0.00 0.00 0|** H
HETATM 5824 H cis 379 34.251 60.594 43.376 0.00 0.00 0|** H
HETATM 5825 H cis 379 35.704 58.271 42.065 0.00 0.00 0|** H
HETATM 5826 H cis 379 36.555 59.526 43.212 0.00 0.00 0|** H
HETATM 5827 H cis 379 36.393 57.750 44.404 0.00 0.00 0|** H
HETATM 5828 H cis 379 34.875 58.831 44.780 0.00 0.00 0|** H
HETATM 5829 H cis 379 33.014 58.166 44.850 0.00 0.00 0|** H
HETATM 5830 H cis 379 32.487 56.942 43.613 0.00 0.00 0|** H
HETATM 5831 H cis 379 33.013 56.397 45.266 0.00 0.00 0|** H
HETATM 5832 H cis 379 34.312 54.940 43.372 0.00 0.00 0|** H
HETATM 5833 H cis 379 36.590 56.671 42.514 0.00 0.00 0|** H
HETATM 5834 H cis 379 36.892 55.394 43.891 0.00 0.00 0|** H
HETATM 5835 H cis 379 36.017 53.814 42.242 0.00 0.00 0|** H
HETATM 5836 H cis 379 36.552 55.201 41.056 0.00 0.00 0|** H
HETATM 5837 H cis 379 38.207 54.980 40.069 0.00 0.00 0|** H
HETATM 5838 H cis 379 39.707 54.990 41.095 0.00 0.00 0|** H
HETATM 5839 H cis 379 39.099 53.429 40.389 0.00 0.00 0|** H
HETATM 5840 H cis 379 39.578 53.099 43.045 0.00 0.00 0|** H
HETATM 5841 H cis 379 38.338 53.658 45.112 0.00 0.00 0|** H
HETATM 5842 H cis 379 36.797 53.776 44.003 0.00 0.00 0|** H
HETATM 5843 H cis 379 36.764 51.556 43.731 0.00 0.00 0|** H
HETATM 5844 H cis 379 38.305 51.439 44.840 0.00 0.00 0|** H
HETATM 5845 H cis 379 35.262 50.329 46.829 0.00 0.00 0|** H
HETATM 5846 H cis 379 37.041 53.636 46.427 0.00 0.00 0|** H
HETATM 5847 H cis 379 35.375 53.046 46.848 0.00 0.00 0|** H
HETATM 5848 H cis 379 36.825 52.370 47.713 0.00 0.00 0|** H
HETATM 5849 H cis 379 36.887 49.717 44.337 0.00 0.00 0|** H
HETATM 5850 H cis 379 36.009 48.542 45.548 0.00 0.00 0|** H
HETATM 5851 H cis 379 34.451 50.243 43.837 0.00 0.00 0|** H
HETATM 5852 H cis 379 35.420 48.747 43.176 0.00 0.00 0|** H
HETATM 5853 H cis 379 33.299 46.269 44.682 0.00 0.00 0|** H
HETATM 5854 H cis 379 32.580 49.975 44.579 0.00 0.00 0|** H
HETATM 5855 H cis 379 31.838 48.440 43.947 0.00 0.00 0|** H
HETATM 5856 H cis 379 32.290 48.577 45.703 0.00 0.00 0|** H
HETATM 5857 H cis 379 36.033 46.625 45.029 0.00 0.00 0|** H
HETATM 5858 H cis 379 35.210 45.399 43.830 0.00 0.00 0|** H
HETATM 5859 H cis 379 35.515 46.797 42.114 0.00 0.00 0|** H
HETATM 5860 H cis 379 36.338 48.024 43.312 0.00 0.00 0|** H
HETATM 5861 H cis 379 38.577 44.851 41.777 0.00 0.00 0|** H
HETATM 5862 H cis 379 38.279 48.091 43.697 0.00 0.00 0|** H
HETATM 5863 H cis 379 39.191 46.525 43.830 0.00 0.00 0|** H
HETATM 5864 H cis 379 39.201 47.452 42.266 0.00 0.00 0|** H
HETATM 5865 H cis 379 35.960 44.090 42.489 0.00 0.00 0|** H
HETATM 5866 H cis 379 35.831 45.306 41.033 0.00 0.00 0|** H
HETATM 5867 H cis 379 36.649 43.967 39.629 0.00 0.00 0|** H
HETATM 5868 H cis 379 37.405 42.895 41.006 0.00 0.00 0|** H
HETATM 5869 H cis 379 35.042 40.380 40.344 0.00 0.00 0|** H
HETATM 5870 H cis 379 33.496 42.029 40.349 0.00 0.00 0|** H
HETATM 5871 H cis 379 33.890 43.476 41.375 0.00 0.00 0|** H
HETATM 5872 H cis 379 34.002 43.588 39.564 0.00 0.00 0|** H
HETATM 5873 H cis 379 37.884 41.448 39.936 0.00 0.00 0|** H
HETATM 5874 H cis 379 37.490 40.606 41.594 0.00 0.00 0|** H
…
I tried to renumber the residues to make them unique, but I got the following error: The following error has occurred while processing one of your PDB files:

Instances of ligand cis do not contain the same atoms.

How can I modify the pdb so that the polyisoprene atoms are unique and are recognized by HADDOCK?

2

See for example: https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451

All atom names within one ligand must be unique

3

To perform this, you can use the pdbtools, pdb_uniqname script: