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What is the format of a PDBQT file?
I've heard that AutoDock 4 uses PDBQT formatted files for the receptor and the ligand. What is the format of a PDBQT file?
AutoGrid 3 uses a
PDBQS file for the receptor, which stores the atomic coordinates, partial charges and solvation parameters for all the atoms in the macromolecule. AutoDock 3 uses a
PDBQ file for the ligand, which stores the atomic coordinates, partial charges and a description of the rigid and rotatable parts of the molecule.
In AutoDock 4, however, we have moved to one format,
PDBQT, which stores the
atomic coordinates, partial charges and AutoDock atom types, for both the receptor and the ligand. This is a big improvement on AutoDock 3 when it comes to atom types: AutoDock 3 determines the atom's type by looking at the first character of the atom name; AutoDock 4 now uses one or two-character names that do not interfere or depend on the atom names. It has also meant we can increase the number of atom types, allowing us to distinguish, for example, between nitrogens that do and do not accept hydrogen bonds, for example.
file must have:
- partial charges.
- AutoDock 4 atom-types.
Both ligand and receptor
PDBQT files used for the standard AutoDock 4 force
field have additional requirements:
- Gasteiger PEOE partial charges.
- A united-atom representation (i.e. only polar hydrogens). A united atom representation can be obtained by first computing the partial charges for an all-hydrogen model of the molecule. Then, for each non-polar heavy atom that has any hydrogens bonded to it, the partial charge of the hydrogen should be added to that of the bonded heavy atom, then this hydrogen atom can be deleted.
Ligands can be treated as flexible in AutoDock, and we use the idea of a
"torsion tree" to represent the rigid and rotatable pieces. There is always one "root", and zero or more "branches". Branches can be nested. Every branch defines one rotatable bond. The torsion tree is represented in the PDBQT with the following records, and the placement of these records is important, and usually means reordering the
ROOTrecord precedes the rigid part of the molecule, from which zero or more rotatable bonds may emanate.
- The rigid root contains one or more PDBQT-style
HETATMrecords. These records resemble their traditional PDB counterparts, but diverge in columns 71-79 inclusive (where the first character in the line corresponds to column 1). The partial charge is stored in columns 71-76 inclusive (in %6.3f format, i.e. right-justified, 6 characters wide, with 3 decimal places). The AutoDock atom-type is stored in columns 78-79 inclusive (in %-2.2s format, i.e. left-justified and 2 characters wide..
ENDROOTrecord follows the last atom in the rigid "root". The
ENDROOTblock of atoms should be given first in the PDBQT file. The simplest way to treat a ligand is rigidly, and this would mean putting a
ROOTrecord before the first
ENDROOTrecord after the last
- Sets of atoms that are moved by rotatable bonds are enclosed by
ENDBRANCHblocks follow the
ENDBRANCHrecords should give two integers separated by spaces, which are the serial numbers of the first and second atoms involved in the rotatable bond. The
BRANCHrecord should be followed by the
HETATMrecord of the second atom in the rotatable bond. It is possible to nest
ENDBRANCHblocks; see the example below.
- The last atom in a branch should be followed by an
ENDBRANCHrecord, whose serial numbers of the two atoms in the rotatable bond should match those in the corresponding
- The last line of the PDBQT file contains a
TORSDOFrecord, which is followed by an integer. This is the number of torsional degrees of freedom in the ligand, and is independent of the number of rotatable bonds, if any, defined by the preceding records.
NOTE: the serial number is the integer in columns 7-11 inclusive of the
HETATM record; the first character in the line corresponds to column 1.
For example, in this PDBQT file, branch 15-21 is nested within branch 9-11, and means there are rotatable bonds between A9 and A11, and also A17 and C21; there is also branch 7-24, with a rotatable bond between A7 and C22:
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 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
This FAQ applies to: AutoDock 4
Is there a limit on the number of atoms in the ligand that can be used in AutoDock?
Is there a limit on the size of the ligand molecule, and if so, how can I change it?
This limit is specified in the source code in the file 'constants.h', by the 'MAX_ATOMS' definition:
#define MAX_ATOMS 2048 /* Maximum number of atoms in Small Molecule. */
The path to the constants file is 'autodocksuite-4.0.1/src/autodock-4.0.1/constants.h'. If you change this line, make sure to change the 'MAX_RECORDS' definition to match the same value as MAX_ATOMS.
This FAQ applies to: AutoDock 3, AutoDock 4
How can I determine if a bond is rotatable in a ligand pdbq(t) file
The flexibility pattern for a ligand is encoded in its written pdbq(t) file by the inclusion of specific AutoDock keywords ROOT/ENDROOT, BRANCH/ENDBRANCH. However, it may not be simple to look at the file and determine which bonds are rotatable and which are not.
- To do so:
- Read the previously-formatted-ligand molecule into ADT using File->Read Molecule
- Choose it to be ligand using Ligand->Choose
- You will then be given the choice of whether or not to 'Use Previous Torsion Tree'
4. You can then see which torsions are active using Ligand->Torsion Tree->Choose Torsions....
- Another way to determine whether a bond is treated as rotatable in ligand pdbq(t) file is to edit the file and look at the BRANCH statements, searching for the numbers of the two atoms in that specific bond. Each BRANCH statement corresponds to one rotatable bond. The BRANCH statement includes the numbers of the corresponding atoms. For example, a bond between atoms numbered 12 and 27 is rotatable if the statement BRANCH 12 27 appears in the pdbq(t) file.
This FAQ applies to: AutoDock 3, AutoDock 4
Virtual Screening CVS Connection problem?
When I try to CVS login, the system tells me "/export/cvs: no such repository"—what's wrong?
The host (moses=>mgl) and the path (/export/cvs=>/opt/cvs) have been changed. If you are using "bash", please use:
If you are using "csh" or "tcsh", use:
setenv CVSROOT :pserver:firstname.lastname@example.org:/opt/cvsVSTutorial.tar.gz (13 MB) - snapshot from CVS created on Jan 25 2008.