MDAnalysis reads coordinates from PDBQT files and additional optional data such as B-factors, partial charge and AutoDock atom types. It is also possible to substitute a PDBQT file for a PSF file in order to define the list of atoms (but no connectivity information will be available in this case).
PDBQTReader that reads a PDBQT-formatted file, no frills.
Original PDB format documentation with AutoDOCK extensions
COLUMNS | DATA TYPE | FIELD | DEFINITION |
---|---|---|---|
1 - 6 | Record name | “CRYST1” | |
7 - 15 | Real(9.3) | a | a (Angstroms). |
16 - 24 | Real(9.3) | b | b (Angstroms). |
25 - 33 | Real(9.3) | c | c (Angstroms). |
34 - 40 | Real(7.2) | alpha | alpha (degrees). |
41 - 47 | Real(7.2) | beta | beta (degrees). |
48 - 54 | Real(7.2) | gamma | gamma (degrees). |
1 - 6 | Record name | “ATOM “ | |
7 - 11 | Integer | serial | Atom serial number. |
13 - 16 | Atom | name | Atom name. |
17 | Character | altLoc | Alternate location indicator. IGNORED |
18 - 21 | Residue name | resName | Residue name. |
22 | Character | chainID | Chain identifier. |
23 - 26 | Integer | resSeq | Residue sequence number. |
27 | AChar | iCode | Code for insertion of residues. IGNORED |
31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. |
39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. |
47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. |
55 - 60 | Real(6.2) | occupancy | Occupancy. |
61 - 66 | Real(6.2) | tempFactor | Temperature factor. |
67 - 76 | Real(10.4) | partialChrg | Gasteiger PEOE partial charge q. |
79 - 80 | LString(2) | atomType | AutoDOCK atom type t. |
We ignore torsion notation and just pull the partial charge and atom type columns:
COMPND NSC7810
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: A7_7 and C22_23
REMARK 2 A between atoms: A9_9 and A11_11
REMARK 3 A between atoms: A17_17 and C21_21
ROOT
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
ATOM 1 A1 INH I 1.054 3.021 1.101 0.00 0.00 0.002 A
ATOM 2 A2 INH I 1.150 1.704 0.764 0.00 0.00 0.012 A
ATOM 3 A3 INH I -0.006 0.975 0.431 0.00 0.00 -0.024 A
ATOM 4 A4 INH I 0.070 -0.385 0.081 0.00 0.00 0.012 A
ATOM 5 A5 INH I -1.062 -1.073 -0.238 0.00 0.00 0.002 A
ATOM 6 A6 INH I -2.306 -0.456 -0.226 0.00 0.00 0.019 A
ATOM 7 A7 INH I -2.426 0.885 0.114 0.00 0.00 0.052 A
ATOM 8 A8 INH I -1.265 1.621 0.449 0.00 0.00 0.002 A
ATOM 9 A9 INH I -1.339 2.986 0.801 0.00 0.00 -0.013 A
ATOM 10 A10 INH I -0.176 3.667 1.128 0.00 0.00 0.013 A
ENDROOT
BRANCH 9 11
ATOM 11 A11 INH I -2.644 3.682 0.827 0.00 0.00 -0.013 A
ATOM 12 A16 INH I -3.007 4.557 -0.220 0.00 0.00 0.002 A
ATOM 13 A12 INH I -3.522 3.485 1.882 0.00 0.00 0.013 A
ATOM 14 A15 INH I -4.262 5.209 -0.177 0.00 0.00 -0.024 A
ATOM 15 A17 INH I -2.144 4.784 -1.319 0.00 0.00 0.052 A
ATOM 16 A14 INH I -5.122 4.981 0.910 0.00 0.00 0.012 A
ATOM 17 A20 INH I -4.627 6.077 -1.222 0.00 0.00 0.012 A
ATOM 18 A13 INH I -4.749 4.135 1.912 0.00 0.00 0.002 A
ATOM 19 A19 INH I -3.777 6.285 -2.267 0.00 0.00 0.002 A
ATOM 20 A18 INH I -2.543 5.650 -2.328 0.00 0.00 0.019 A
BRANCH 15 21
ATOM 21 C21 INH I -0.834 4.113 -1.388 0.00 0.00 0.210 C
ATOM 22 O1 INH I -0.774 2.915 -1.581 0.00 0.00 -0.644 OA
ATOM 23 O3 INH I 0.298 4.828 -1.237 0.00 0.00 -0.644 OA
ENDBRANCH 15 21
ENDBRANCH 9 11
BRANCH 7 24
ATOM 24 C22 INH I -3.749 1.535 0.125 0.00 0.00 0.210 C
ATOM 25 O2 INH I -4.019 2.378 -0.708 0.00 0.00 -0.644 OA
ATOM 26 O4 INH I -4.659 1.196 1.059 0.00 0.00 -0.644 OA
ENDBRANCH 7 24
TORSDOF 3
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
Read coordinates from filename.
filename can be a gzipped or bzip2ed compressed PDBQT file.
PDBQT writer that implements a subset of the PDB 3.2 standard and the PDBQT spec.
Write ATOM record. http://www.wwpdb.org/documentation/format32/sect9.html Only some keyword args are optional (altLoc, iCode, chainID), for some defaults are set.
All inputs are cut to the maximum allowed length. For integer numbers the highest-value digits are chopped (so that the serial and reSeq wrap); for strings the trailing characters are chopped.
Note: Floats are not checked and can potentially screw up the format.
Write CRYST1 record. http://www.wwpdb.org/documentation/format32/sect8.html
Write generic REMARK record (without number). http://www.wwpdb.org/documentation/format32/remarks1.html http://www.wwpdb.org/documentation/format32/remarks2.html
Write TITLE record. http://www.wwpdb.org/documentation/format32/sect2.html