AutoDock Changelog

What's new in AutoDock 4.2.6

• To increase consistency across platforms, all executable programs (both autogrid and autodock) are compiled using double-precision arithmetic. The grid maps, as read by AutoDock, are stored internally in single-precision.
• Multiple search methods are now possible in a single AutoDock job: such as 20 runs using Simulated Annealing, 20 runs using the Genetic Algorithm, and 20 runs using local-search-only. The runs are done serially and no results "carry over" from one method to another. However, all results are ranked and clustered together in the
• analysis step at the end of the entire job.
• You can now use ADT (AutoDock Tools) to visualize results from AutoDock jobs that use simulated annealing or local-search-only. You must download the latest build of ADT from http://mgltools.scripps.edu/downloads/latest
• Note a limitation in the 4.2.6 release: the "do_local_only" command runs the pseudo-solis-wets algorithm, even if the solis-wets has been specified using "set_local sw1". This applies only to "do_local_only": the "ga_run" command will use whichever local search has been specified. (We recommend the pseudo-solis-wets for all local searches: "set psw1").
• AutoDock calculations are performed as a series of independent runs. Users will occasionally need to repeat a run. For example, they might want to repeat a particular run to examine the search space and convergence of that run. AutoDock now reports the specific random number seeds used for each run. Any specific run can be repeated exactly by using the random number seeds reported in the prior calculation.
• The docking log file (.dlg) contents have been further standardized: Regardless of 'outlev' setting, the host name, run date, working directory, and names of input PDBQT files are reported at the beginning of the AutoDock job. Each 'run' (GA, LGA, local search, simulated annealing) reports its initial random number seeds and its ending total energy and state in a uniform format suitable for automated analysis. At outlev setting "BASIC" (0) or above, the initial PDBQT ligand (and flexres, if present)
• coordinates are reported. At outlev setting "ADT" (1) or above, the final docked coordinates of each run are reported.
• Some advanced autodock users customize the program for their own specific needs. We've improved and simplified building AutoDock and AutoGrid from source files. We have documented the process of compiling new atomic parameter tables into AutoDock and AutoGrid in the README file included in this distribution.
• We continue to improve AutoDock's robustness and stability. AutoDock now verifies that all its input grid maps are the same size.
• If AutoDock's standard input has not been redirected to come from a file or from a pipe, you must specify a docking parameter file using "-p ". When the docking parameters are read from standard input (e.g., "autodock4 -l mol.dlg < mol.dpf"), the docking parameter file now appears in output PDBQT files as "stdin". Reading and parsing the input PDBQT coordinate files has been made more robust.
• Other changes:
• Improved error checking of command-line arguments.
• Better checking of the atom numbers that define internal and "flexres" torsions.
• Better cross-platform compatibility of the internal random number generator.
• Running "autodock4 (or autogrid4) --version" reports compile-time configuration options.