When I performed the docking between my ligand and protein, but it went wrong. It was written as follow:
Error in PDB file.
Issue when parsing the PDB file at line 1 .
Your PDB contains an elemental ion CD without specified charge
I tried everything I can to correct the pdb file, but it didn’t work. Can anyone tell me where I got it wrong? Many thanks in advance. Wish you all luck. My pdb file is as follow:
HETATM 1 CD+2 CD A 801 -86.676 31.102 125.481 0.00 0.00 CD
HETATM 2 C EB4 A 802 -86.723 30.514 128.103 0.00 0.00 C
HETATM 3 N EB4 A 802 -89.520 30.521 128.960 0.00 0.00 N
HETATM 4 O EB4 A 802 -87.209 31.370 127.209 0.00 0.00 O
HETATM 5 C EB4 A 802 -87.508 33.591 125.091 0.00 0.00 C
HETATM 6 N EB4 A 802 -90.312 34.242 126.037 0.00 0.00 N
HETATM 7 O EB4 A 802 -87.972 32.338 125.192 0.00 0.00 O
HETATM 8 C EB4 A 802 -88.220 29.532 123.876 0.00 0.00 C
HETATM 9 N EB4 A 802 -91.377 30.081 124.177 0.00 0.00 N
HETATM 10 O EB4 A 802 -88.028 29.917 125.208 0.00 0.00 O
HETATM 11 C EB4 A 802 -85.667 29.746 127.481 0.00 0.00 C
HETATM 12 O EB4 A 802 -85.349 29.936 126.204 0.00 0.00 O
HETATM 13 C EB4 A 802 -86.122 33.659 125.307 0.00 0.00 C
HETATM 14 O EB4 A 802 -85.525 32.511 125.563 0.00 0.00 O
HETATM 15 C EB4 A 802 -87.080 29.874 123.115 0.00 0.00 C
HETATM 16 O EB4 A 802 -86.149 30.599 123.796 0.00 0.00 O
HETATM 17 C EB4 A 802 -84.893 28.899 128.328 0.00 0.00 C
HETATM 18 O EB4 A 802 -88.763 30.864 131.186 0.00 0.00 O
HETATM 19 C EB4 A 802 -85.510 34.919 125.145 0.00 0.00 C
HETATM 20 O EB4 A 802 -90.482 35.739 124.118 0.00 0.00 O
HETATM 21 C EB4 A 802 -87.051 29.564 121.790 0.00 0.00 C
HETATM 22 O EB4 A 802 -91.355 27.712 123.633 0.00 0.00 O
HETATM 23 C EB4 A 802 -85.351 28.620 129.618 0.00 0.00 C
HETATM 24 O EB4 A 802 -93.364 30.236 129.115 0.00 0.00 O
HETATM 25 C EB4 A 802 -86.320 36.090 124.985 0.00 0.00 C
HETATM 26 O EB4 A 802 -93.324 34.071 128.232 0.00 0.00 O
HETATM 27 C EB4 A 802 -88.137 28.981 121.135 0.00 0.00 C
HETATM 28 O EB4 A 802 -94.591 31.425 125.724 0.00 0.00 O
HETATM 29 C EB4 A 802 -86.549 29.182 130.087 0.00 0.00 C
HETATM 30 O EB4 A 802 -91.472 32.719 128.014 0.00 0.00 O
HETATM 31 C EB4 A 802 -87.747 35.988 124.806 0.00 0.00 C
HETATM 32 O EB4 A 802 -92.392 32.266 125.618 0.00 0.00 O
HETATM 33 C EB4 A 802 -89.345 28.854 121.880 0.00 0.00 C
HETATM 34 O EB4 A 802 -91.799 30.324 127.229 0.00 0.00 O
HETATM 35 C EB4 A 802 -87.167 30.254 129.425 0.00 0.00 C
HETATM 36 C EB4 A 802 -88.348 34.728 124.791 0.00 0.00 C
HETATM 37 C EB4 A 802 -89.364 29.015 123.273 0.00 0.00 C
HETATM 38 C EB4 A 802 -88.449 31.072 129.833 0.00 0.00 C
HETATM 39 C EB4 A 802 -89.856 34.548 124.614 0.00 0.00 C
HETATM 40 C EB4 A 802 -90.554 28.817 124.145 0.00 0.00 C
HETATM 41 C EB4 A 802 -90.948 30.877 129.457 0.00 0.00 C
HETATM 42 C EB4 A 802 -91.719 34.494 126.369 0.00 0.00 C
HETATM 43 C EB4 A 802 -92.658 29.978 124.905 0.00 0.00 C
HETATM 44 C EB4 A 802 -91.973 29.973 128.613 0.00 0.00 C
HETATM 45 C EB4 A 802 -91.997 34.045 127.839 0.00 0.00 C
HETATM 46 C EB4 A 802 -93.352 31.407 124.937 0.00 0.00 C
HETATM 47 C EB4 A 802 -91.275 32.359 129.368 0.00 0.00 C
HETATM 48 C EB4 A 802 -92.749 33.683 125.547 0.00 0.00 C
HETATM 49 C EB4 A 802 -92.597 29.421 126.365 0.00 0.00 C
CONECT 1 4 7 10 12
CONECT 1 14 16
CONECT 2 4 11 35
CONECT 3 38 41 49
CONECT 4 1 2
CONECT 5 7 13 36
CONECT 6 39 42
CONECT 7 1 5
CONECT 8 10 15 37
CONECT 9 40 43
CONECT 10 1 8
CONECT 11 2 12 17
CONECT 12 1 11
CONECT 13 5 14 19
CONECT 14 1 13
CONECT 15 8 16 21
CONECT 16 1 15
CONECT 17 11 23
CONECT 18 38
CONECT 19 13 25
CONECT 20 39
CONECT 21 15 27
CONECT 22 40
CONECT 23 17 29
CONECT 24 44
CONECT 25 19 31
CONECT 26 45
CONECT 27 21 33
CONECT 28 46
CONECT 29 23 35
CONECT 30 45 47
CONECT 31 25 36
CONECT 32 46 48
CONECT 33 27 37
CONECT 34 44 49
CONECT 35 2 29 38
CONECT 36 5 31 39
CONECT 37 8 33 40
CONECT 38 3 18 35
CONECT 39 6 20 36
CONECT 40 9 22 37
CONECT 41 3 44 47
CONECT 42 6 45 48
CONECT 43 9 46 49
CONECT 44 24 34 41
CONECT 45 26 30 42
CONECT 46 28 32 43
CONECT 47 30 41
CONECT 48 32 42
CONECT 49 3 34 43
END