Property calculation for Guassian input structure

Hello CXN Team,

Here is a simple query. I have imported a "guassian cube" format file. I have tried calculating properties using calculator plugins, but it displayed an error message as below. Is that one should not calculate properties for a guassian import structure. Please correct if I am wrong.

Error message below.

chemaxon.marvin.plugin.PluginException: Calculation result is not defined for query molecules: [#6]~[#8]~[#6]~1~[#6]~[#6](~[#8]~[#6])~[#6]~2~[#6](~[#6]~1)~[#6](~[#8])~[#6](~[#6])~[#6]~1~[#6]~3~[#6]~[#6]~4~[#8]~[#6](~[#8])~[#6]~[#8](~[#6])~[#6]~4~[#6]~[#6]~3~[#8]~[#6]~[#6]~2~1
 at chemaxon.marvin.plugin.CalculatorPlugin.checkMolecule(Unknown Source)
 at chemaxon.marvin.calculations.pKaPlugin.checkMolecule(Unknown Source)
 at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
 at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
 at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
 at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
 at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
 at chemaxon.marvin.common.swing.MolPanel$5.run(Unknown Source)

Thanks & regards,

Yogitha

 

 

 

Hi Yogitha,

Most of the calculator plugins cannot calculate properties for query molecules. In these cases the error message is "Calculation result is not defined for query molecules.".

Gaussian Cube file format does not store bond information, so the bonds are imported as ANY bond (see Gaussian Cube format help). ANY bond is a query bond type, the imported molecules are query molecules.

You can use the "b" Gaussian Cube format import option (see Gaussian Cube import options) to guess the bond types, atom charges and implicit hydrogens from atom distances and valence rules (Warning: This is an experimental feature).

Regards,
Zsolt

Zsolt wrote:

Hi Yogitha, Most of the calculator plugins cannot calculate properties for query molecules. In these cases the error message is "Calculation result is not defined for query molecules.". Gaussian Cube file format does not store bond information, so the bonds are imported as ANY bond (see Gaussian Cube format help). ANY bond is a query bond type, the imported molecules are query molecules. You can use the "b" Gaussian Cube format import option (see Gaussian Cube import options) to guess the bond types, atom charges and implicit hydrogens from atom distances and valence rules (Warning: This is an experimental feature). Regards, Zsolt

Hi Zsolt,

Yes, bonds in the guassian imported structure appear as any bond. Thanks much for the reply.

Regards,

Yogitha