Hello,
I am using the easy interface on the web server to dock a protein to a RNA structure, and I am receiving the following error:
First pdb file contains multiple residues with number 35 in chain A
I’ve successfully used a similar RNA structure with HADDOCK once before. I searched the forum and found a post concerning the same error but the solution did not solve my problem. I have tried many different changes to residue 35 in the PDB file and to the whole PDB file. I still keep receiving the same error. Residue 35 is the last nucleotide residue in the PDB.
I saw that you have a script to format pdbs on your github page. Can I use this script even if I don’t have a local version of HADDOCK on my machine?
I appreciate any help you can provide.
Thanks in advance
-Kendy
Below is the end of the PDB file starting at residue 35 (columns are aligned when file opened in vi)
ATOM 741 O1 CYT A 35 -16.552 1.663 -0.357 1.00 67.73 O
ATOM 742 O2 CYT A 35 -15.312 2.627 -2.388 1.00 57.22 O
ATOM 743 O’ CYT A 35 -17.801 2.757 -2.207 1.00 74.54 O
ATOM 744 C’ CYT A 35 -19.032 2.535 -1.534 1.00 71.70 C
ATOM 745 C’ CYT A 35 -20.226 2.662 -2.452 1.00 70.58 C
ATOM 746 O’ CYT A 35 -20.208 3.928 -3.160 1.00 68.66 O
ATOM 747 C’ CYT A 35 -20.354 1.632 -3.561 1.00 66.94 C
ATOM 748 O3’ CYT A 35 -20.820 0.373 -3.102 1.00 67.82 O
ATOM 749 C2’ CYT A 35 -21.308 2.321 -4.534 1.00 61.70 C
ATOM 750 C2’ CYT A 35 -22.652 2.202 -4.094 1.00 55.96 O
ATOM 751 C1’ CYT A 35 -20.880 3.789 -4.398 1.00 57.81 C
ATOM 752 N1 CYT A 35 -19.981 4.216 -5.496 1.00 52.54 N
ATOM 753 C2 CYT A 35 -20.554 4.566 -6.723 1.00 48.58 C
ATOM 754 O2 CYT A 35 -21.787 4.521 -6.840 1.00 44.52 O
ATOM 755 N3 CYT A 35 -19.754 4.953 -7.745 1.00 43.24 N
ATOM 756 C4 CYT A 35 -18.431 4.988 -7.575 1.00 38.29 C
ATOM 757 N4 CYT A 35 -17.673 5.371 -8.603 1.00 37.27 N
ATOM 758 C5 CYT A 35 -17.819 4.633 -6.339 1.00 38.48 C
ATOM 759 C6 CYT A 35 -18.623 4.255 -5.336 1.00 42.70 C
HETATM 761 K+1 K1 C 36 -15.791 26.462 -8.453 1.00 39.16 K
HETATM 762 K+1 K1 C 37 -16.170 29.934 -8.429 1.00 15.94 K
HETATM 763 K+1 K1 C 38 -16.135 33.213 -8.262 1.00 17.71 K
HETATM 764 K+1 K1 C 39 -16.449 -18.230 -31.428 1.00 89.08 K
END