12 January 2024 3 3K Report

Hello,

I am using Autodock4 and AGFR to perform in silico docking experiments with a small molecule, triptolide, and a human protein, XPB (ERCC3). I am running on windows 11. I only experience this issue when performing docking with flexible residues.

I prepared the ligand file using the Autodock Tools interface. The prepared ligand file is below:

REMARK 2 active torsions:

REMARK status: ('A' for Active; 'I' for Inactive)

REMARK 1 A between atoms: C_4 and C_2

REMARK 2 A between atoms: O_23 and C_17

ROOT

ATOM 1 C UNL d 1 29.320 -35.802 -65.656 0.00 0.00 0.010 C

ATOM 2 C UNL d 1 30.655 -36.509 -65.505 0.00 0.00 0.020 C

ATOM 3 C UNL d 1 31.481 -36.415 -66.786 0.00 0.00 0.010 C

ENDROOT

BRANCH 2 4

ATOM 4 C UNL d 1 31.414 -35.962 -64.276 0.00 0.00 0.129 A

ATOM 5 C UNL d 1 32.206 -34.626 -64.232 0.00 0.00 0.186 C

ATOM 6 C UNL d 1 33.144 -34.610 -63.021 0.00 0.00 0.156 A

ATOM 7 O UNL d 1 33.172 -33.137 -63.096 0.00 0.00 -0.359 OA

ATOM 8 C UNL d 1 34.431 -33.885 -63.005 0.00 0.00 0.157 A

ATOM 9 C UNL d 1 32.606 -35.189 -61.637 0.00 0.00 0.138 A

ATOM 10 C UNL d 1 35.436 -34.297 -61.794 0.00 0.00 0.043 C

ATOM 11 C UNL d 1 34.996 -35.365 -60.947 0.00 0.00 0.030 C

ATOM 12 C UNL d 1 33.528 -35.393 -60.451 0.00 0.00 0.009 C

ATOM 13 C UNL d 1 36.026 -35.404 -59.931 0.00 0.00 -0.019 C

ATOM 14 C UNL d 1 33.535 -33.891 -60.010 0.00 0.00 0.015 C

ATOM 15 C UNL d 1 33.129 -35.753 -59.204 0.00 0.00 0.015 C

ATOM 16 C UNL d 1 34.291 -35.969 -58.106 0.00 0.00 0.043 C

ATOM 17 C UNL d 1 35.635 -35.641 -58.522 0.00 0.00 0.039 C

ATOM 18 C UNL d 1 36.885 -35.753 -57.845 0.00 0.00 0.336 C

ATOM 19 O UNL d 1 37.997 -35.493 -58.737 0.00 0.00 -0.457 OA

ATOM 20 O UNL d 1 37.016 -36.031 -56.771 0.00 0.00 -0.245 OA

ATOM 21 C UNL d 1 37.485 -35.611 -60.106 0.00 0.00 0.264 C

ATOM 22 C UNL d 1 31.529 -36.108 -61.742 0.00 0.00 0.186 A

ATOM 23 O UNL d 1 31.351 -34.850 -61.074 0.00 0.00 -0.358 OA

ATOM 24 C UNL d 1 31.536 -36.827 -63.142 0.00 0.00 0.185 A

ATOM 25 O UNL d 1 32.525 -36.859 -64.163 0.00 0.00 -0.359 OA

BRANCH 5 26

ATOM 26 O UNL d 1 31.029 -33.875 -64.291 0.00 0.00 -0.386 OA

ATOM 27 H UNL d 1 31.242 -32.949 -64.278 0.00 0.00 0.210 HD

ENDBRANCH 5 26

ENDBRANCH 2 4

TORSDOF 2

I entered the following command into the command line:

C:\Users\gorri\OneDrive\Desktop\Fan Lab\Docking\Autodock4\HsXPB\HsXPB_7NVVSite2FlexReceptors&EnlargeGridtoBoxFlexResidues>autodock4 -p dockywocky.dpf -l results.dlg

Then I get the following error message:

autodock4: FATAL ERROR: autodock4: ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 39 in PDBQT file "TLI_model.pdbqt".

So, then I changed the ligand file to the following to force it to work:

ATOM 1 C UNL d 1 29.320 -35.802 -65.656 0.00 0.00 0.010 C

ATOM 2 C UNL d 1 30.655 -36.509 -65.505 0.00 0.00 0.020 C

ATOM 3 C UNL d 1 31.481 -36.415 -66.786 0.00 0.00 0.010 C

ATOM 4 C UNL d 1 31.414 -35.962 -64.276 0.00 0.00 0.129 A

ATOM 5 C UNL d 1 32.206 -34.626 -64.232 0.00 0.00 0.186 C

ATOM 6 C UNL d 1 33.144 -34.610 -63.021 0.00 0.00 0.156 A

ATOM 7 O UNL d 1 33.172 -33.137 -63.096 0.00 0.00 -0.359 OA

ATOM 8 C UNL d 1 34.431 -33.885 -63.005 0.00 0.00 0.157 A

ATOM 9 C UNL d 1 32.606 -35.189 -61.637 0.00 0.00 0.138 A

ATOM 10 C UNL d 1 35.436 -34.297 -61.794 0.00 0.00 0.043 C

ATOM 11 C UNL d 1 34.996 -35.365 -60.947 0.00 0.00 0.030 C

ATOM 12 C UNL d 1 33.528 -35.393 -60.451 0.00 0.00 0.009 C

ATOM 13 C UNL d 1 36.026 -35.404 -59.931 0.00 0.00 -0.019 C

ATOM 14 C UNL d 1 33.535 -33.891 -60.010 0.00 0.00 0.015 C

ATOM 15 C UNL d 1 33.129 -35.753 -59.204 0.00 0.00 0.015 C

ATOM 16 C UNL d 1 34.291 -35.969 -58.106 0.00 0.00 0.043 C

ATOM 17 C UNL d 1 35.635 -35.641 -58.522 0.00 0.00 0.039 C

ATOM 18 C UNL d 1 36.885 -35.753 -57.845 0.00 0.00 0.336 C

ATOM 19 O UNL d 1 37.997 -35.493 -58.737 0.00 0.00 -0.457 OA

ATOM 20 O UNL d 1 37.016 -36.031 -56.771 0.00 0.00 -0.245 OA

ATOM 21 C UNL d 1 37.485 -35.611 -60.106 0.00 0.00 0.264 C

ATOM 22 C UNL d 1 31.529 -36.108 -61.742 0.00 0.00 0.186 A

ATOM 23 O UNL d 1 31.351 -34.850 -61.074 0.00 0.00 -0.358 OA

ATOM 24 C UNL d 1 31.536 -36.827 -63.142 0.00 0.00 0.185 A

ATOM 25 O UNL d 1 32.525 -36.859 -64.163 0.00 0.00 -0.359 OA

ATOM 26 O UNL d 1 31.029 -33.875 -64.291 0.00 0.00 -0.386 OA

ATOM 27 H UNL d 1 31.242 -32.949 -64.278 0.00 0.00 0.210 HD

TORSDOF 2

I then get the following error message:

autodock4: FATAL ERROR: autodock4: ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 1 in PDBQT file "TLI_model.pdbqt".

Any help is greatly appreciated. Thank you.

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