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cxcalc conformer option problem
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Tobias

Joined: 26 Jan 2005
Posts: 580

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Link to postPosted: Thu Sep 20, 2007 10:29 pmPost subject: cxcalc conformer option problem Reply with quote

Hi,
I a had some molecules and tried to use optimization level 1, 2, 3 ,4 (hyperfine?) to generate lowest energy conformers. So I generated a file with O1 level, then put the O1 level into O2 level, O2 level into O3 level, O3 into O4 level, but this level can not be generated due to the error message below.

Some of the results even with the high optimization levels also had higher energies (i think around 3% of the molecules), so I tried to generate a statistics from it and then later transfer the molecules to the free MOPAC2007 which not only had the AM1 and PM3, but also PM6. This is actually a nice work for a workflow.


Z:\>cxcalc conformers happymolecules-ok-3D-O3.sdf -O 4 -m 1 -f sdf > happymolecules-ok-3D-O4.sdf
ERROR IN OPTIONS: Invalid optimization limit. Use an integer between 0 and 4
ERROR IN OPTIONS: Unable to parse optimization limit. Use an integer between 0 and 4
Error at molecule: 1 ID = 1
java.lang.UnsupportedOperationException: Unable to parse optimization limit. Use an integer between 0 and 4
java.lang.UnsupportedOperationException: Unable to parse optimization limit. Use an integer between 0 and 4
at chemaxon.marvin.modules.Clean3D.reportOptionError(Clean3D.java:504)
at chemaxon.marvin.modules.Clean3D.processOptionL(Clean3D.java:547)
at chemaxon.marvin.modules.Clean3D.processOption(Clean3D.java:689)
at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:857)
at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3279)
at chemaxon.struc.Molecule.clean(Molecule.java:592)
at chemaxon.marvin.calculations.ConformerPlugin.calculateConformers(ConformerPlugin.java:405)
at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:250)
at chemaxon.marvin.calculations.ConformerPluginOutput.getResult(ConformerPluginOutput.java:60)
at chemaxon.marvin.Calculator.run(Calculator.java:880)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)

Tobias
Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

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Link to postPosted: Fri Sep 21, 2007 10:24 amPost subject: Reply with quote

Hi,

Code:
$ cxcalc conformers -h

Calculator plugin: conformers.

Calculates the conformers of the molecule.

Usage:
  cxcalc [general options] [input files/strings] conformers
[conformers options] [input files/strings]

conformers options:
  -h, --help            this help message
  -f, --format          <output format> should be a 3D format (default: sdf)
  -m, --maxconformers   <maximum number of conformers to be generated>
                        (default: 100)
  -d, --diversity       <diversity limit> (default: 0.1)
  -s, --saveconfdesc    [true|false] if true a single conformer is saved
                        with a property containing conformer information
                        (default: false)
  -e, --hyperfine       [true|false] if true hyperfine option is set
                        (default: false)
  -y, --prehydrogenize  [true|false] if true prehydrogenize is done before
                        calculation, if false calculation is done without
                        hydrogens (default: true)
  -l, --timelimit       <timelimit for calculation in sec> (default: 900)
  -O, --optimization    [0|1|2|3] conformer generation optimiztaion limit
                        for different enviroments
                        {0}: very loose  (limit=0.01)
                        {1}: normal      (limit=0.0010)
                        {2}: strict      (limit=1.0E-4)
                        {3}: very strict (limit=1.0E-5)
                        (default: 1)

Multiple values for the same parameter
should be separated by commas (',' without space).

Example:
  cxcalc conformers -m 250 -s true test.sdf


Only 0,1,2 or 3 is accepted as parameter for the optimization limit, see the command line help above.

Code:
ERROR IN OPTIONS: Invalid optimization limit. Use an integer between 0 and 4
ERROR IN OPTIONS: Unable to parse optimization limit. Use an integer between 0 and 4
Error at molecule: 1 ID = 1


The error message is not correct, we will correct it. Thanks for the report.

Zsolt
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