qikprop Command Help

Command: $SCHRODINGER/qikprop

Usage: qikprop [<options>] <input-file>

   <input-file> - The file containing the structures to be treated.
                  The file format is inferred from the file suffix;
                  Recognized suffixes: .mol, .sdf, .mol2, .pdb, .z,
                                            .mae, mae.gz and .maegz

Options:
   -fast        - Run job in fast mode (no dipole, homo or lumo).
   -nofast      - Run job in standard mode (default).
   -nofailout   - Return in output CSV and structure files only compounds
                  that successfully were processed by QikProp.  By default
                  each input compound input is included in the output.
   -neut        - Neutralize molecules in Maestro formatted files prior
                  to processing (default).
   -noneut      - Suppress neutralization of molecules in Maestro
                  formatted files prior to processing.
   -n <X:Y>     - Process only molecules numbered X to Y.
   -outcomp     - Compress output structure (Maestro and mol only)
   -outname <name> - Override basename in naming output files.
   -altclass    - Run additional SASA, PSA calculations using an
                  alternative class definition
   -altprobe    - Run additional SASA, PSA calculations using an
                  alternative probe radii (1.4A by default)
   -sim         - Generate a list of known drugs most similar to
                  each processed molecule (default).
   -nosim       - Supress generation of a list of known drugs most
                  similar to each processed molecule.
   -recap         Replace the CombiGlide functional group with a methyl
                  group prior to processing.  When used in the CombiGlide
                  reagent-preparation process, gives properties for
                  the 'naked sidechain'.
   -nosa        - Suppress generation of .qpsa output file.
   -simf        - Generate a file of the <n> most similar drug molecules
                  to the last molecule processed.
   -nsim <int>  - Number of the most similar drug molecules to report.
                  (default=5)
   -simdb <file>  - Use alternative drug-like similarity database.
   -logpdb <file> - Use alternative logP similarity database.
   -logsdb <file> - Use alternative logS similarity database.
    
   -HOST <host> - Run job on a remote host.
   -LOCAL       - Run the job in the current directory, rather than
                    in a temporary scratch directory
   -WAIT        - Do not return until the job completes.
   -NICE        - Run the job at reduced priority.
    
   -DEBUGGER <debugger program with debugger args>
                - Run QikProp in the foreground with the debugger
                    called <debuger program> with its arguments.
        
   -HELP        - Print this message and exit.