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Missing atom types (“Why atom type 'X' is not recognized?”)

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This FAQ applies to: Any version.

AutoDock has been parameterized to support atom types that are most frequently encountered in biological systems, and were included in the complexes used to calibrate the force field. For this reason, many of the less common atom types are not included in the force field parameters. There are several ways of dealing with this problem, depending on the trade between the level of complexity involved in modeling them and accuracy obtained: The rigorous way. Find appropriate parameters for the new atom type and add them to the existing forcefield parameter file. AutoGrid and AutoDock may then be run using parameters from the file instead of the internal parameters. The format for the parameter file is described in full in the AutoDock Manual. This process can be simplified by modifying one of the existing atom types and simply changing the vdW radii to give an approximate set of parameters. The easy way. Substitute the atom type with the closest type already present in the existing forcefield (for instance, using C or A for boron). This change is made by manually changing the PDBQT file, substituting the atom type of the atom with an existing atom type. The atomic charge may also be set manually.

The next AutoDock release will include extended atom types and it will simplify the process of adding missing atom types.

by Sargis Dallakyan last modified 2012-11-26 14:51
Contributors: Stefano Forli

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