.. -*- coding: utf-8 -*-
.. _PDBQT-format:
=======================================
PDBQT (Autodock structure)
=======================================
.. include:: classes/PDBQT.txt
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)
.. _PDBQT:
https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
.. _AutoDock:
http://autodock.scripps.edu/
Writing out
===========
MDAnalysis implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec. Unlike the :ref:`PDB-format` writer, MDAnalysis cannot write multi-frame trajectories to a PDBQT file.
If the Universe is missing fields that are :ref:`required in a PDBQT file <pdbqt-spec>`, MDAnalysis provides default values and raises a warning. There are 2 exceptions to this:
- ``chainIDs``: if a Universe does not have ``chainIDs``, MDAnalysis uses the first character of the segment ``segid`` 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
.. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _PDBQT: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
.. _pdbqt-spec:
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 documentation:
http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _AutoDOCK extensions:
http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
.. table:: 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)