PDBQT (Autodock structure)¶
Coordinate reader |
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Coordinate writer |
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Topology parser |
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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 havechainIDs, MDAnalysis uses the first character of the segmentsegidinstead.
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
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)