Dear Professor Bonvin and HADDOCK team,
I am trying to dock small molecule, which I have generated the pdb via RD-kit, to a protein. However, I have been encountering with “There was an error in the topology generation.The most likely cause is an unusual format of your PDB structures.” problem. I have already tried to use pdb-tools tidy and validate scripts to tidy it. This is a chemical structure containing 2 rings. I am suspecting this error might be caused by misproper numbering of carbons. Also, I suspected maybe the conformation generated was not proper and used pdb containing all 33 different conformers. However, resulted with the same error This is the pdb
"
HETATM 1 N1 LIG 1 2.294 -0.116 0.601 1.00 0.00
HETATM 2 N2 LIG 1 2.512 1.591 -1.055 1.00 0.00
HETATM 3 N3 LIG 1 0.618 2.409 -2.246 1.00 0.00
HETATM 4 N4 LIG 1 -2.877 -1.016 0.409 1.00 0.00
HETATM 5 C1 LIG 1 6.313 -1.110 1.415 1.00 0.00
HETATM 6 C2 LIG 1 5.346 -1.227 2.405 1.00 0.00
HETATM 7 C3 LIG 1 4.022 -0.882 2.119 1.00 0.00
HETATM 8 C4 LIG 1 5.968 -0.664 0.143 1.00 0.00
HETATM 9 C5 LIG 1 4.643 -0.321 -0.140 1.00 0.00
HETATM 10 C6 LIG 1 3.655 -0.394 0.852 1.00 0.00
HETATM 11 C7 LIG 1 1.719 0.743 -0.375 1.00 0.00
HETATM 12 C8 LIG 1 1.923 2.382 -1.954 1.00 0.00
HETATM 13 C20 LIG 1 0.330 0.676 -0.610 1.00 0.00
HETATM 14 C9 LIG 1 -0.164 1.558 -1.579 1.00 0.00
HETATM 20 C15 LIG 1 -1.932 -0.187 -0.238 1.00 0.00
HETATM 15 C10 LIG 1 -1.524 1.554 -1.868 1.00 0.00
HETATM 16 C11 LIG 1 -2.415 0.692 -1.221 1.00 0.00
HETATM 17 C12 LIG 1 -4.318 1.374 -2.545 1.00 0.00
HETATM 18 C13 LIG 1 -4.618 2.755 -2.146 1.00 0.00
HETATM 19 C14 LIG 1 -4.860 3.885 -1.819 1.00 0.00
HETATM 21 C16 LIG 1 -2.662 -1.892 1.449 1.00 0.00
HETATM 22 C17 LIG 1 -3.918 -2.585 1.857 1.00 0.00
HETATM 23 C18 LIG 1 -3.915 -3.468 2.864 1.00 0.00
HETATM 24 C19 LIG 1 -0.568 -0.202 0.049 1.00 0.00
HETATM 25 O1 LIG 1 -3.769 0.629 -1.452 1.00 0.00
HETATM 26 O2 LIG 1 -1.602 -2.110 2.020 1.00 0.00
HETATM 27 CL1 LIG 1 7.159 -0.544 -1.096 1.00 0.00
HETATM 28 F LIG 1 7.578 -1.447 1.707 1.00 0.00
TER
END
"
When I further check error message on topology generation I found following error:
" POWELL: STEP number limit. Normal termination
POWELL: Current coordinates set to last minimum
SELRPN: 2 atoms have been selected out of 30
SELRPN: 2 atoms have been selected out of 30
SELRPN: 2 atoms have been selected out of 30
DCART: temperature coupling (TCOUpling) enabled
%CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%%
improper energy constant missing.
target improper value missing.
periodicity missing.
ATOM1: SEGId=" ", RESId="1 ", NAME="N1 “, CHEMical=“NAAA”
ATOM2: SEGId=” ", RESId="1 ", NAME="C7 ", CHEMical=“CA6 "
ATOM3: SEGId=” ", RESId="1 ", NAME="HAA “, CHEMical=“HAAA”
ATOM4: SEGId=” ", RESId="1 ", NAME="C6 “, CHEMical=“CAAJ”
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%%
improper energy constant missing.
target improper value missing.
periodicity missing.
ATOM1: SEGId=” ", RESId="1 ", NAME="C7 ", CHEMical=“CA6 "
ATOM2: SEGId=” ", RESId="1 ", NAME="N2 ", CHEMical=“NA1 "
ATOM3: SEGId=” ", RESId="1 ", NAME="N1 “, CHEMical=“NAAA”
ATOM4: SEGId=” ", RESId="1 ", NAME="C20 ", CHEMical="CA5 "
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CODIMP error encountered: program will be aborted.
(CNS is in mode: SET ABORT=NORMal END)
ABORT mode will terminate program execution.
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 9860352 bytes
Maximum dynamic memory overhead: 1664 bytes
Program started at: 16:08:29 on 29-Aug-2022
Program stopped at: 16:08:29 on 29-Aug-2022
CPU time used: 0.2173 seconds
============================================================
"
You can also find the image of the ligand attached.
Thanks in advance!