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My ligand contain Cu2+ atom in it. when i am trying to generate .str file in cgenff its showing error. when i tried to check my pdb file in charmm gui its also showing error that not able to read CU2+.
So can anyone tell me what i should do.
here error in charmm gui
Error parsing HETAT, expected chain ID at column 22, but got ‘’:
HETATM 1 CU2P 0 1.699 21.234 -13.605 1.00 0.00 LIG CU2P
here i have attached my pdb file for reference.
HETATM 1 CU2P 0 1.699 21.234 -13.605 1.00 0.00 LIG CU2P
HETATM 2 O17 0 3.490 21.104 -12.856 1.00 0.00 LIG O
HETATM 3 O16 0 -0.195 21.277 -13.979 1.00 0.00 LIG O
HETATM 4 O12 0 4.633 19.982 -11.310 1.00 0.00 LIG O
HETATM 5 N9 0 1.196 19.889 -12.207 1.00 0.00 LIG N
HETATM 6 O15 0 -2.116 21.142 -12.867 1.00 0.00 LIG O
HETATM 7 C11 0 3.570 20.359 -11.806 1.00 0.00 LIG C
HETATM 8 C10 0 2.234 19.987 -11.174 1.00 0.00 LIG C
HETATM 9 C13 0 -0.162 20.308 -11.790 1.00 0.00 LIG C
HETATM 10 C14 0 -0.913 20.939 -12.977 1.00 0.00 LIG C
HETATM 11 C8 0 1.122 18.512 -12.789 1.00 0.00 LIG C
HETATM 12 C2 0 2.359 18.105 -13.522 1.00 0.00 LIG C
HETATM 13 C3 0 3.410 17.483 -12.862 1.00 0.00 LIG C
HETATM 14 C4 0 4.540 17.022 -13.520 1.00 0.00 LIG C
HETATM 15 C5 0 4.621 17.290 -14.889 1.00 0.00 LIG C
HETATM 16 C19 0 5.613 16.251 -12.813 1.00 0.00 LIG C
HETATM 17 C6 0 3.627 17.956 -15.589 1.00 0.00 LIG C
HETATM 18 C20 0 3.783 18.271 -17.071 1.00 0.00 LIG C
HETATM 19 C7 0 2.501 18.356 -14.897 1.00 0.00 LIG C
HETATM 20 O18 0 3.199 17.277 -11.502 1.00 0.00 LIG O
HETATM 21 H18 0 3.416 18.016 -11.096 1.00 4.82 LIG H
HETATM 22 O21 0 2.167 22.601 -14.871 1.00 0.00 LIG O
HETATM 23 H21 0 2.654 22.263 -15.485 1.00 5.84 LIG H
HETATM 24 H21 0 1.457 22.923 -15.221 1.00 5.84 LIG H
CONECT 1 2
CONECT 1 22
CONECT 1 3
CONECT 1 5
CONECT 2 7
CONECT 3 10
CONECT 4 7
CONECT 5 8
CONECT 5 9
CONECT 5 11
CONECT 6 10
CONECT 7 8
CONECT 9 10
CONECT 11 12
CONECT 12 19
CONECT 12 13
CONECT 13 14
CONECT 13 20
CONECT 14 16
CONECT 14 15
CONECT 15 17
CONECT 17 18
CONECT 17 19
CONECT 20 21
CONECT 22 23
CONECT 22 24
thank you