PDBQT Files

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.

Format Definition

A complete PDBQT 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 ATOM/HETATM records:

1. A ROOT record precedes the rigid part of the molecule, from which zero or more rotatable bonds may emanate.
2. The rigid root contains one or more PDBQT-style ATOM or HETATM records. 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..
3. An ENDROOT record follows the last atom in the rigid "root". The ROOT/ENDROOT block 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 ROOT record before the first ATOM/HETATM and an ENDROOT record after the last ATOM/HETATM.
4. Sets of atoms that are moved by rotatable bonds are enclosed by BRANCH and ENDBRANCH records. These BRANCH/ENDBRANCH blocks follow the ROOT/ENDROOT block. Both BRANCH records and ENDBRANCH records should give two integers separated by spaces, which are the serial numbers of the first and second atoms involved in the rotatable bond. The BRANCH record should be followed by the ATOM/HETATM record of the second atom in the rotatable bond. It is possible to nest BRANCH/ENDBRANCH blocks; see the example below.
5. The last atom in a branch should be followed by an ENDBRANCH record, whose serial numbers of the two atoms in the rotatable bond should match those in the corresponding BRANCH record.
6. The last line of the PDBQT file contains a TORSDOF record, 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 ATOM or 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

Yes, there is a limit on the number of atoms in the ligand.  By default, the maximum number of atoms is 2048.

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.

The overall flexibility pattern encoded in a ligand pdbq(t) file can visualized using ADT.

• To do so:

1. Read the previously-formatted-ligand molecule into ADT using File->Read Molecule
2. Choose it to be ligand using Ligand->Choose
3. You will then be given the choice of whether or not to  'Use Previous Torsion Tree'

=> choose Yes
    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.

The host (moses=>mgl) and the path (/export/cvs=>/opt/cvs) have been changed. If you are using "bash", please use:

export CVSROOT=:pserver:anonymous@mgl1.scripps.edu:/opt/cvs

If you are using "csh" or "tcsh", use:

setenv CVSROOT :pserver:anonymous@mgl1.scripps.edu:/opt/cvs

http://mgltools.scripps.edu/documentation/how-to/access-to-cvs

You can also download VSTutorial.tar.gz (13 MB) - snapshot from CVS created on Jan 25 2008.