# proteinprep interface file !BRIEF [ []] !CATEGORY "input/output options :" 1 !PARAMETER -in 1 !ALIAS -i !TYPE string !BRIEF Input molecule filename (must have 3D coordinates) !SIMPLE true !REQUIRED true !KEYLESS 1 !END !PARAMETER -cplxout 2 !ALIAS -p !TYPE string !DEFAULT proteinprep.oeb.gz !BRIEF Output complex filename !SIMPLE true !REQUIRED false !KEYLESS 2 !END !PARAMETER -ligout 3 !ALIAS -l !TYPE string !BRIEF Output ligand filename !SIMPLE true !REQUIRED false !KEYLESS 3 !END !END !CATEGORY "Calculation options :" 2 !PARAMETER -alts 1 !TYPE string !LEGAL_VALUE occupancy !LEGAL_VALUE a !LEGAL_VALUE ignore !LEGAL_VALUE compare !DEFAULT occupancy !BRIEF Alternate location atom handling (affects atom:atom interactions) !SIMPLE true !REQUIRED false !DETAIL occupancy - keep just the highest average occupancy for each alt group a - keep only loc code A (and blank) ignore - assume alts already selected appropriately compare - keep all alts but only interact if same loc code (or blank) !END !PARAMETER -placehydrogens 2 !TYPE bool !DEFAULT true !BRIEF If false, hydrogens will not be added !SIMPLE true !REQUIRED false !END !PARAMETER -waterprocessing 3 !TYPE string !LEGAL_VALUE ignore !LEGAL_VALUE focused !LEGAL_VALUE fullsearch !DEFAULT fullsearch !BRIEF How waters are processed !SIMPLE true !REQUIRED false !DETAIL ignore - leave water hydrogens in a random orientation focused - search orientations based on neighboring polar groups fullsearch - do an extensive search of water orientations !END !PARAMETER -standardizehyd 4 !ALIAS -stdhyd !TYPE bool !DEFAULT true !BRIEF If false, bonds for hydrogens are not adjusted to standard lengths !SIMPLE false !REQUIRED false !END !PARAMETER -clashcutoff 5 !TYPE double !DEFAULT 0.4 !BRIEF Van der Waals overlap (in Angstroms) defined to be a bad clash !SIMPLE false !REQUIRED false !END !PARAMETER -flipbias 6 !TYPE double !DEFAULT 1.0 !BRIEF Scale factor for the bias against flipping sidechains such as HIS !SIMPLE false !REQUIRED false !END !PARAMETER -maxsubstates 7 !TYPE double !DEFAULT 1.0e8 !BRIEF Maximum number of substates in a single step of hydrogen placement optimization !SIMPLE false !REQUIRED false !END !END !CATEGORY "Display options :" 9 !PARAMETER -verbose 1 !ALIAS -v !TYPE bool !DEFAULT false !BRIEF Display more information about the process !SIMPLE true !REQUIRED false !END !END