PDBQT (Autodock structure)

Coordinate reader

MDAnalysis.coordinates.PDBQT.PDBQTReader

Coordinate writer

MDAnalysis.coordinates.PDBQT.PDBQTWriter

Topology parser

MDAnalysis.topology.PDBQTParser.PDBQTParser

Reading in

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).

Although PDBQT is a similar file format to PDB, MDAnalysis treats them with several differences:

  • Multi-model PDBQT files are not supported

  • Connectivity is not supported (i.e. bonds are not read)

Writing out

MDAnalysis implements a subset of the PDB 3.2 standard and the PDBQT spec. Unlike the PDB, ENT (Standard PDB file) writer, MDAnalysis cannot write multi-frame trajectories to a PDBQT file.

If the Universe is missing fields that are required in a PDBQT file, MDAnalysis provides default values and raises a warning. There are 2 exceptions to this:

  • chainIDs: if a Universe does not have chainIDs, MDAnalysis will use the segids instead.

  • elements: MDAnalysis uses the atom type as the element.

These are the default values:

  • names: ‘X’

  • altLocs: ‘’

  • resnames: ‘UNK’

  • icodes: ‘’

  • segids: ‘’

  • resids: 1

  • occupancies: 1.0

  • tempfactors: 0.0

  • types (elements): ‘’

  • charges: 0.0

PDBQT specification

Records read:
  • CRYST1 for unit cell dimensions A,B,C, alpha,beta,gamma

  • ATOM or HETATM for serial, name, resName, chainID, resSeq, x, y, z, occupancy, tempFactor, segID

PDB format with AutoDOCK extensions for the PDBQT format.

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 - 70

LString(4)

footnote

Usually blank. IGNORED.

71 - 76

Real(6.4)

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)