convert_single_ligand_pdbqt_to_pdb.py does not convert the pdbqt to pdb format #8
Description
I try to use the above mentioned command to convert the .pdbqt format to .pdb format but it does not do the conversion
Here is an example .pdbqt I want to convert to .pdb format using the command
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C3_3 and O1_4
REMARK 2 A between atoms: O1_4 and C4_5
REMARK 3 A between atoms: C5_6 and N1_7
REMARK 4 A between atoms: C6_10 and N4_11
REMARK 5 A between atoms: C7_14 and N7_15
ROOT
HETATM 1 C1 LIG X 999 3.938 -1.278 0.258 1.00 0.00 0.014 C
HETATM 2 C2 LIG X 999 3.514 -0.491 -0.550 1.00 0.00 -0.091 C
HETATM 3 C3 LIG X 999 2.991 0.465 -1.532 1.00 0.00 0.268 C
ENDROOT
BRANCH 3 4
HETATM 4 O1 LIG X 999 1.649 0.129 -1.879 1.00 0.00 -0.336 OA
BRANCH 4 5
HETATM 5 C4 LIG X 999 0.577 0.277 -0.988 1.00 0.00 0.115 A
HETATM 6 C5 LIG X 999 0.129 1.562 -0.637 1.00 0.00 0.161 A
HETATM 7 C6 LIG X 999 -0.928 1.711 0.298 1.00 0.00 0.159 A
HETATM 8 C7 LIG X 999 -1.509 0.559 0.890 1.00 0.00 0.138 A
HETATM 9 C8 LIG X 999 -1.126 -0.732 0.447 1.00 0.00 0.011 A
HETATM 10 C9 LIG X 999 -1.797 -1.897 0.882 1.00 0.00 0.015 A
HETATM 11 C13 LIG X 999 -0.065 -0.867 -0.484 1.00 0.00 0.013 A
HETATM 12 C10 LIG X 999 -1.387 -3.160 0.453 1.00 0.00 0.001 A
HETATM 13 C11 LIG X 999 -0.316 -3.288 -0.427 1.00 0.00 0.001 A
HETATM 14 C12 LIG X 999 0.338 -2.151 -0.900 1.00 0.00 0.015 A
BRANCH 6 15
HETATM 15 N1 LIG X 999 0.760 2.679 -1.293 1.00 0.00 -0.067 NA
HETATM 16 N2 LIG X 999 0.435 3.857 -1.135 1.00 0.00 -0.162 NA
HETATM 17 N3 LIG X 999 0.117 5.036 -0.984 1.00 0.00 0.068 N
ENDBRANCH 6 15
BRANCH 7 18
HETATM 18 N4 LIG X 999 -1.350 3.039 0.665 1.00 0.00 -0.067 NA
HETATM 19 N5 LIG X 999 -2.425 3.294 1.210 1.00 0.00 -0.162 NA
HETATM 20 N6 LIG X 999 -3.498 3.557 1.751 1.00 0.00 0.068 N
ENDBRANCH 7 18
BRANCH 8 21
HETATM 21 N7 LIG X 999 -2.451 0.725 1.962 1.00 0.00 -0.069 NA
HETATM 22 N8 LIG X 999 -2.344 0.109 3.024 1.00 0.00 -0.162 NA
HETATM 23 N9 LIG X 999 -2.238 -0.504 4.085 1.00 0.00 0.068 N
ENDBRANCH 8 21
ENDBRANCH 4 5
ENDBRANCH 3 4
TORSDOF 5
I get the following format which is not the pdb format
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C3_3 and O1_4
REMARK 2 A between atoms: O1_4 and C4_5
REMARK 3 A between atoms: C5_6 and N1_7
REMARK 4 A between atoms: C6_10 and N4_11
REMARK 5 A between atoms: C7_14 and N7_15
ROOT
HETATM 1 C1 LIG X 999 3.938 -1.278 0.258 1.00 0.00 0.014 C
HETATM 2 C2 LIG X 999 3.514 -0.491 -0.550 1.00 0.00 -0.091 C
HETATM 3 C3 LIG X 999 2.991 0.465 -1.532 1.00 0.00 0.268 C
ENDROOT
BRANCH 3 4
HETATM 4 O1 LIG X 999 1.649 0.129 -1.879 1.00 0.00 -0.336 OA
BRANCH 4 5
HETATM 5 C4 LIG X 999 0.577 0.277 -0.988 1.00 0.00 0.115 A
HETATM 6 C5 LIG X 999 0.129 1.562 -0.637 1.00 0.00 0.161 A
HETATM 7 C6 LIG X 999 -0.928 1.711 0.298 1.00 0.00 0.159 A
HETATM 8 C7 LIG X 999 -1.509 0.559 0.890 1.00 0.00 0.138 A
HETATM 9 C8 LIG X 999 -1.126 -0.732 0.447 1.00 0.00 0.011 A
HETATM 10 C9 LIG X 999 -1.797 -1.897 0.882 1.00 0.00 0.015 A
HETATM 11 C13 LIG X 999 -0.065 -0.867 -0.484 1.00 0.00 0.013 A
HETATM 12 C10 LIG X 999 -1.387 -3.160 0.453 1.00 0.00 0.001 A
HETATM 13 C11 LIG X 999 -0.316 -3.288 -0.427 1.00 0.00 0.001 A
HETATM 14 C12 LIG X 999 0.338 -2.151 -0.900 1.00 0.00 0.015 A
BRANCH 6 15
HETATM 15 N1 LIG X 999 0.760 2.679 -1.293 1.00 0.00 -0.067 NA
HETATM 16 N2 LIG X 999 0.435 3.857 -1.135 1.00 0.00 -0.162 NA
HETATM 17 N3 LIG X 999 0.117 5.036 -0.984 1.00 0.00 0.068 N
ENDBRANCH 6 15
BRANCH 7 18
HETATM 18 N4 LIG X 999 -1.350 3.039 0.665 1.00 0.00 -0.067 NA
HETATM 19 N5 LIG X 999 -2.425 3.294 1.210 1.00 0.00 -0.162 NA
HETATM 20 N6 LIG X 999 -3.498 3.557 1.751 1.00 0.00 0.068 N
ENDBRANCH 7 18
BRANCH 8 21
HETATM 21 N7 LIG X 999 -2.451 0.725 1.962 1.00 0.00 -0.069 NA
HETATM 22 N8 LIG X 999 -2.344 0.109 3.024 1.00 0.00 -0.162 NA
HETATM 23 N9 LIG X 999 -2.238 -0.504 4.085 1.00 0.00 0.068 N
ENDBRANCH 8 21
ENDBRANCH 4 5
ENDBRANCH 3 4
TORSDOF 5
When I load it in the VMD I could see the first three atoms instead of the whole ligand
The same is the case with convert_vina_docked_pdbqt_to_pdbs.py command.