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--- bend:pdbqt_example [2020/03/24 18:19]
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+A complete PDBQT file must have partial charges, and 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, and 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:
+  - A ROOT record 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 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.
+  - 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.
+  - 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.
+  - 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.
+  - 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.
 This file was manually generated using AutoDock tools (adt), following the tutorial video from AutoDock Vina: http://vina.scripps.edu/tutorial.html

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