SZMAP documentation

This is the documentation of SZMAP

Major Changes

  • The Water Orientation VIDA Extension (version 1.1.3) now displays the correct water orientations for results from szmap version 1.2.0. Previous versions of the extension will show random orientations for waters from these results.
  • The Water Orientation VIDA Extension now saves orientation probability data and ensemble energy, vdw and order data on probe molecules as SDData. When probes generated by this extension are written to an .sdf file, these values will be written as well.
  • gameplan no longer crashes when all stabilization test sites clash.
  • pch no longer treats CYS residues bonded through the sidechain to a non-CYS as anionic and no longer duplicates non-standard groups containing a metal (such as cofactors) and groups they are bonded to. The option -nonsymmetrized_charges now works correctly to control AM1BCC partial charges but now defaults to true so as to not alter the default behavior.

For the complete list of features and bug fixes, please refer to the Release Notes chapter. You can find out more about our applications and toolkits in OpenEye Products

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This documentation was updated on June 19, 2015.

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