I am facing fatal error when I am running autoduck4. Please suggest me how I can fix this error
C:/Users/Public/Autodocking/autodock4: FATAL ERROR: C:/Users/Public/Autodocking/autodock4: ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 25 in PDBQT file "ligand.pdbqt".
C:/Users/Public/Autodocking/autodock4: Unsuccessful Completion.
You are not being very helpful to us. Any time your problem is explained in a single sentence or two, chances are that you didn't provide enough detail to help us help you.
Some basic things: what is the command you entered when the error occurred? Did you look into your ligand file?
ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 25 in PDBQT file "ligand.pdbqt".
This is a pretty clear error message - it says that ATOM lines must come before BRANCH lines. Is that the case in your ligand file, and if not, how did you make that file?
If you actually did all of this (the error is clear as to which file is wrong) and entered the required information in your question, we'd be answering it instead of breaking down the error message word by word.
first i prepare pdbqt file of ligand and protein then prepare gpf file, dpf file. after that i run autogrid diretctly ( Run>autogrid), than(run>autodock4)....i am facing this issue its my ligand.pdbqt file
REMARK 5 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: O2_2 and C9_9 REMARK 2 A between atoms: O3_3 and C10_10 REMARK 3 A between atoms: O4_4 and C13_13 REMARK 4 A between atoms: N7_7 and C11_11 REMARK 5 A between atoms: C12_12 and C13_13 ROOT HETATM 1 O1 SUB 1 -1.365 -0.541 1.022 0.00 0.00 -0.353 OA HETATM 2 C9 SUB 1 -1.367 0.971 -0.802 0.00 0.00 0.198 C HETATM 3 C10 SUB 1 -2.797 0.576 -0.499 0.00 0.00 0.182 C HETATM 4 C11 SUB 1 -0.654 0.585 0.482 0.00 0.00 0.263 C HETATM 5 C12 SUB 1 -2.610 -0.701 0.308 0.00 0.00 0.179 C ENDROOT BRANCH 4 6 HETATM 6 N7 SUB 1 0.713 0.210 0.259 0.00 0.00 -0.280 N HETATM 7 C14 SUB 1 1.741 1.172 0.398 0.00 0.00 0.331 A HETATM 8 O5 SUB 1 1.541 2.348 0.709 0.00 0.00 -0.246 OA HETATM 9 N8 SUB 1 3.037 0.698 0.156 0.00 0.00 -0.275 N HETATM 10 C17 SUB 1 3.397 -0.594 -0.198 0.00 0.00 0.250 A HETATM 11 O6 SUB 1 4.549 -0.963 -0.401 0.00 0.00 -0.268 OA HETATM 12 C16 SUB 1 2.265 -1.535 -0.322 0.00 0.00 0.092 A HETATM 13 C15 SUB 1 1.025 -1.098 -0.094 0.00 0.00 0.104 A ENDBRANCH 4 6 HETATM 14 O2 SUB 1 -1.243 2.347 -1.101 0.00 0.00 -0.388 OA BRANCH 5 15 HETATM 15 C13 SUB 1 -2.503 -1.950 -0.557 0.00 0.00 0.198 C HETATM 16 O4 SUB 1 -2.322 -3.073 0.288 0.00 0.00 -0.398 OA ENDBRANCH 5 15 HETATM 17 O3 SUB 1 -3.409 1.547 0.350 0.00 0.00 -0.390 OA TORSDOF 5
It is impossible to read through your ligand file because it is not properly formatted. Please tell me which line in that file is 25th based on what you provided?
When you paste the lines that need to be formatted, you select them and click on the button that says 101010 which will format them. When it looks like the .pdbqt file I pasted below, it is much easier to inspect the contents.
REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C2'_10 and O2'_11
REMARK 2 A between atoms: C1'_13 and N9_14
REMARK 3 A between atoms: C6_19 and N6_20
REMARK 4 A between atoms: C2'_38 and O2'_39
REMARK 5 A between atoms: C1'_41 and N9_42
REMARK 6 A between atoms: C6_47 and N6_48
REMARK 7 A between atoms: C2'_66 and O2'_67
REMARK 8 A between atoms: C1'_69 and N9_70
REMARK 9 A between atoms: C6_75 and N6_76
REMARK 10 A between atoms: C2'_94 and O2'_95
REMARK 11 A between atoms: C1'_97 and N9_98
REMARK 12 A between atoms: C6_103 and N6_104
ROOT
ATOM 1 P A C 1 -15.532 -69.520 -2.464 1.00125.22 0.408 P
ATOM 2 OP1 A C 1 -15.575 -69.043 -3.862 1.00124.72 -0.624 OA
ATOM 3 OP2 A C 1 -14.759 -68.759 -1.457 1.00121.99 -0.624 OA
ATOM 4 O5' A C 1 -15.020 -71.056 -2.479 1.00129.94 -0.287 OA
ATOM 5 C5' A C 1 -13.732 -71.415 -2.993 1.00130.77 0.216 C
ATOM 6 C4' A C 1 -12.700 -71.194 -1.902 1.00132.63 0.180 C
ATOM 7 O4' A C 1 -13.108 -71.866 -0.671 1.00133.57 -0.353 OA
ATOM 8 C3' A C 1 -11.351 -71.808 -2.297 1.00133.33 0.198 C
ATOM 9 O3' A C 1 -10.322 -70.839 -2.045 1.00131.78 -0.279 OA
ATOM 10 C2' A C 1 -11.222 -72.966 -1.338 1.00133.85 0.199 C
ATOM 11 C1' A C 1 -11.865 -72.337 -0.114 1.00135.60 0.262 C
ATOM 12 P A C 2 -9.044 -70.710 -2.990 1.00132.86 0.408 P
ATOM 13 OP1 A C 2 -8.592 -72.069 -3.367 1.00131.82 -0.624 OA
From what I can tell, your ligand has no ATOM lines, which is probably why it doesn't work. My guess is that the initial PDB file from which you extracted the ligand was incorrect, but really tough to tell based on the limited information you provided.
It is too time-consuming when we have to troubleshoot everything one thing at a time, especially when you are not responding to my questions and suggestions. You will have to figure this one out on your own.
I will repeat: it is likely to be an issue with your original PDB ligand file, or whatever was used to make ligand.pdbqt. That file has only HETATM lines, which is clearly wrong because carbons, oxygens and nitrogens are not heteroatoms. Besides, that SUB in place of chain and residue identifiers is likely to be wrong as well. You have above how a proper ligand file should look like, so I suggest you work with your input until you can get something similar to it. Maybe replacing HETATM with ATOM will fix it. In case it is not clear, there should be two empty spaces after ATOM to make the number of characters equal after replacement.
first i prepare pdbqt file of ligand and protein then prepare gpf file, dpf file. after that i run autogrid diretctly ( Run>autogrid), than(run>autodock4)....i am facing this issue its my ligand.pdbqt file
REMARK 5 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: O2_2 and C9_9 REMARK 2 A between atoms: O3_3 and C10_10 REMARK 3 A between atoms: O4_4 and C13_13 REMARK 4 A between atoms: N7_7 and C11_11 REMARK 5 A between atoms: C12_12 and C13_13 ROOT HETATM 1 O1 SUB 1 -1.365 -0.541 1.022 0.00 0.00 -0.353 OA HETATM 2 C9 SUB 1 -1.367 0.971 -0.802 0.00 0.00 0.198 C HETATM 3 C10 SUB 1 -2.797 0.576 -0.499 0.00 0.00 0.182 C HETATM 4 C11 SUB 1 -0.654 0.585 0.482 0.00 0.00 0.263 C HETATM 5 C12 SUB 1 -2.610 -0.701 0.308 0.00 0.00 0.179 C ENDROOT BRANCH 4 6 HETATM 6 N7 SUB 1 0.713 0.210 0.259 0.00 0.00 -0.280 N HETATM 7 C14 SUB 1 1.741 1.172 0.398 0.00 0.00 0.331 A HETATM 8 O5 SUB 1 1.541 2.348 0.709 0.00 0.00 -0.246 OA HETATM 9 N8 SUB 1 3.037 0.698 0.156 0.00 0.00 -0.275 N HETATM 10 C17 SUB 1 3.397 -0.594 -0.198 0.00 0.00 0.250 A HETATM 11 O6 SUB 1 4.549 -0.963 -0.401 0.00 0.00 -0.268 OA HETATM 12 C16 SUB 1 2.265 -1.535 -0.322 0.00 0.00 0.092 A HETATM 13 C15 SUB 1 1.025 -1.098 -0.094 0.00 0.00 0.104 A ENDBRANCH 4 6 HETATM 14 O2 SUB 1 -1.243 2.347 -1.101 0.00 0.00 -0.388 OA BRANCH 5 15 HETATM 15 C13 SUB 1 -2.503 -1.950 -0.557 0.00 0.00 0.198 C HETATM 16 O4 SUB 1 -2.322 -3.073 0.288 0.00 0.00 -0.398 OA ENDBRANCH 5 15 HETATM 17 O3 SUB 1 -3.409 1.547 0.350 0.00 0.00 -0.390 OA TORSDOF 5
It is impossible to read through your ligand file because it is not properly formatted. Please tell me which line in that file is 25th based on what you provided?
When you paste the lines that need to be formatted, you select them and click on the button that says
101010which will format them. When it looks like the .pdbqt file I pasted below, it is much easier to inspect the contents.From what I can tell, your ligand has no
ATOMlines, which is probably why it doesn't work. My guess is that the initial PDB file from which you extracted the ligand was incorrect, but really tough to tell based on the limited information you provided.It is too time-consuming when we have to troubleshoot everything one thing at a time, especially when you are not responding to my questions and suggestions. You will have to figure this one out on your own.
I will repeat: it is likely to be an issue with your original PDB ligand file, or whatever was used to make
ligand.pdbqt. That file has onlyHETATMlines, which is clearly wrong because carbons, oxygens and nitrogens are not heteroatoms. Besides, thatSUBin place of chain and residue identifiers is likely to be wrong as well. You have above how a proper ligand file should look like, so I suggest you work with your input until you can get something similar to it. Maybe replacingHETATMwithATOMwill fix it. In case it is not clear, there should be two empty spaces after ATOM to make the number of characters equal after replacement.