NEW IN DOCK 6.2 ###Grid Reading Memory Efficiency### The various DOCK classes that handle grid reading and analysis have been refactored. As a direct result, grids are now only read once and then accessed by various scoring functions, thus significantly reducing the memory used when multiple grid-based scoring functions are called. ###Conformation Output Control### In version DOCK 6.1, we forced writing of all scored conformations. We have since found that this option significantly increases the length of the calculation and can take up inappropriate amounts of disk space for large libraries. Previously, the parameter num_scored_conformers_written controlled both the number of conformations scored by the primary scoring function, as well as the number of conformations written. In the new release, these two functions have been decoupled into two user parameters: num_scored_conformers, which sets the number of conformations to be scored by the primary scoring function, and write_conformations, which controls whether these conformations will be written. Similarly, num_secondary_scored_conformers_written has been decoupled into num_secondary_scored_conformers and write_secondary_conformations. These changes provide users with greater control over conformation output. ###Continuous Score Distance Dependent Dielectric Control### The distance dependence of the dielectric factor in the electrostatic term of the continuous score of DOCK can now be switched off via input parameter cont_score_use_dist_dep_dielectric. ###Amber Score Improvements### The error reporting and robustness of the Amber score preparation scripts have been improved. If any step in the amberization fails fatally then termination is immediate. Detection of parmchk "ATTN, needs revision" messages for missing force field parameters and a recovery/override mechanism for the frcmod files have been added. The recovery process is described in the warning message and involves creating a ligand_prefix.frcmod.revised file. The override mechanism is the file parameters/leap/cmd/leaprc.dock.user that is now sourced by every amberization script. Automatic support for a simple treatment of metal ions based on Amber's ff94 has been added: parameters/leap/cmd/leaprc.dock.ions. A library that is automatically used has been started for common cofactors: parameters/leap/cmd/leaprc.dock.cofactors. Support for RNA receptors has been added. The new script prepare_rna_amber.pl differs from prepare_amber.pl only in that the former assumes that any nucleic acids are RNA whereas the latter assumes DNA. Minimization convergence criterion specification via input parameter amber_score_minimization_rmsgrad has been added. In verbose mode Amber score now emits at every step (ntpr=1). Skipping of inadequately prepped ligands via the input parameter amber_score_abort_on_unprepped_ligand has been added. ###Sphere Selector### The total number of spheres is now unlimited, eliminating the previous maximum of 100000 spheres. ###Miscellaneous### Incremental improvements in documentation, installation, and testing. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DEPRECATED FEATURES 1. For a variety of reasons still under active development, amber_score cannot effectively be used as a secondary_score. This function was temporarily deprecated in 6.1, and using input parameter amber_score_secondary causes program termination. The recommended protocol is to perform two DOCK runs with the second run specifying amber_score as the primary_score. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUG FIXES Some bug reports have not yet been processed, but several important bugs have been fixed since the last release. For DOCK: Ensure all cliques are examined as orients including the last one. Incorrect electrostatics with gbsa_hawkins_score_cont_vdw_and_es = yes. Incorrect communication of the Amber score ligand identifier. Memory leak in Amber score due to absent freeing of nab molecules. Incorrect documenting and handling of the charge options in amberize_ligand. Memory leak in PBSA score. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INPUT PARAMETER CHANGES Added: amber_score_minimization_rmsgrad 0.01 amber_score_abort_on_unprepped_ligand yes cont_score_use_dist_dep_dielectric yes num_scored_conformers 1 num_secondary_scored_conformers 1 write_secondary_conformations yes Removed: num_scored_conformers_written 1 num_secondary_scored_conformers_written 1