Name

Unix Synopsis

Description

For a complete description of the Rubicon algorithm and options, see the "Rubicon Reference Manual." The following is an excerpt from its "Introduction" chapter:

"Rubicon" stands for "RUle-Based Invention of CONformations". Rubicon is a distance-geometry method which produces 3-D conformations given chemical structures with only connectivity specified. Distance-geometry methods randomly sample conformations and are particularly powerful for problems dealing with molecular matching and flexibility. The method has three basic parts: establishing geometric constraints in distance-space, sampling a conformation in that space, and embedding it in 3-dimensions while minimizing bounds violations.

One of the fundamental difficulties with most distance distance geometry programs is that they have a very naive view of chemical geometry. Also, the chemical intelligence that they do have is typically hard coded into the program and is very difficult to improve upon. Rubicon addresses this problem by employing a soft, rule-based method for establishing geometric constraints which is based on a powerful language for describing chemical patterns (SMARTS).

Options

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Acceptable RMS of gradient vector for convergence

Acceptable maximum distance violation, Angstroms

Acceptable maximum volume violation, cubic Angstroms

Effective machine accuracy

(Don't) apply VDW bumping to nonbonded 1-4 distances

QUIET ..... no output on standard error
TERSE ..... only show progress
ERRORS .... also show error messages
WARNINGS .. also show warning messages
NOTES ..... also show notes
DEBUG ..... also show debugging output
VERBOSE ... also show all debugging output

(Don't) enforce chirality in conformation filter.

Minimum distance between equivalent atoms to consider conformations non-identical, Angstroms (off if 0.0).

SMARTS used for conformation filter atom matching. If "USMILES", unique SMILES is used as target.

ALL ....... include all hydrogens
SOME ...... include specified hydrogens
NONE ...... suppress all normal hydrogens

Limit function evaluations allowed per minimization

Number of conformations generated for each molecule

TDT ....... Write output in TDT format
PDB ....... write output in PDB format

Name(s) of Rubicon rule file(s) Rubicon rule file names typically end .rules Quote if multiple, e.g. -RUBE_RULES "a.rules b.rules"

Add $D3DG generation item with runid to TDT output. If set to "NONE", $D3DG item will not be output.

Random number seed in range 0 to 900000000

Number of trials per conformation

Add smoothed distance bounds matrix and list of volume bounds to output (TDT output only).

Return Value

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Files

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