error in geometry tools

Hi,

I am newbie and have a question.

I use geometry tools in Marvin Sketch 5.5.01 for my structure (file attached). but error message appeared:

ERROR:

Cannot run plugin: Geometry

[BUG] Optimization was not converged.

 

STACK TRACE:

java.lang.UnsupportedOperationException: [BUG] Optimization
was not converged.

                at
chemaxon.calculations.ProjectedSurfaceArea.optimize(Unknown Source)

                at chemaxon.calculations.ProjectedSurfaceArea.run(Unknown
Source)

                at
chemaxon.calculations.Geometry.calculateMoleculeProjection(Unknown Source)

                at
chemaxon.marvin.calculations.GeometryPlugin.run(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)

 

please help, ASAP !

regards,

Dwi

Hi Dwi,

I could reproduce the bug you have found. Thank you for the report.  A quick fix is to untick the "Set projection optimization" option in the "Tools\Geometry\Geometry options" window before launching the calculation.

 

Regards,

Adrian

Hi Adrian,

Thank you for the quick respond for my problem.

I have tried your suggestion for the structure and several others, it worked nicely for all of them.

Now, more questions :-)

this "projection optimization", what does it mean? does it affecting the structure of the molecule? in what way?

 

Regards,

Dwi

Hi Dwi,

This option does not affects the (3d) structure of the molecule. It is used in the minimal/maximal projected surface area calculation.

Minimum and maximum projected surface area is expected to correlate membrane permability (eg.: blood brain barrier penetration).

Projected surface area is the area of the 2d projection of the 3d molecule. The algorithm finds the extrema of this area by calculating projection of discrete orientations of the molecule. Once the optimization is option is selected a numerical optimizer is used to fine tune the orientation found as best for min and max.

Regards,

Adrian

Hi Adrian,

Is it OK if I assume that the geometry calculation is based on the most stable shape of the molecule? (In my case above, the two carbon chains forming a "V" shape). How do I know that it is the most stable shape?

If I want to arrange the carbon chains as close as possible (parallel ?) and do the geometry calculation, what should I do?

Regards,

Dwi

Hi Dwi, please find my reply inline. hudiyanti wrote:

Hi Adrian, Is it OK if I assume that the geometry calculation is based on the most stable shape of the molecule? (In my case above, the two carbon chains forming a "V" shape). How do I know that it is the most stable shape? Getting the lowest energy conformation (the most stable shape) is not a trivial task for a molecule. For molecules having only a few rotatable bonds that is doable but for flexible chains this can be a hard task. We have two issues here: Accuracy level of energy calculation. Quantum chemistry/Semi empirical/force field and the algorithm to change conformations a and search the lowest. There are many good books on this topic. In marvin sketch there is a simple conformational analysis tool under Tools/Conformation/Conformer  menu.  If I want to arrange the carbon chains as close as possible (parallel ?) and do the geometry calculation, what should I do? Are the two chains connected or two fragments? In the latter case unfortunately the intermolecular interactions between are not considered in the current version. Regards, Dwi

I hope this was helpful.

Adrian

Hi Adrian,

I attach a drawing to discribe my last question:

If I want to arrange the carbon chains as close as possible (parallel ?) and do the geometry calculation, what should I do?

what I meant is: suppose I want to do the geometry calculation for the molecule with its carbon chains are in the position 2 (please see the drawing). what should I do?

regards,

Dwi

Hi Dwi,

I see your point. Here is what I would do:

1. Temporary connect every second atom in the chain : see 1.png and 2.png (the newly inserted bonds are AnyBonds in the figure just to be easily differentiable. Single bond type should also work)

2. depending on 2D or 3D structure you need choose 2-2D or 2-3D steps.

2-2D: press [ctrl]-2 in MarvinSketch . When the structure is cleaned remove the newly inserted bonds. And you are done.

2-3D:

1. Be sure that Structure\Clean3d\Cleaning Method\Fine Build is selected


2. press [ctrl]-3 in MarvinSketch. When 3D structure is generated remove the newly inserted bonds. You can rotate the structure after pressing [F7].


3. Select Structure\Clean3d\Cleaning Method\Gradient optimize and press again [ctrl]-3


4. set back the original:Structure\Clean3d\Cleaning Method\Fine Build for later use


5. Done

Hi Adrian,

I have done your instruction to my structures. It worked the way I wanted. Thank you.

Regards,

Dwi

Hi Adrian,

I have just notice that when I choose Maximal distance perpendicular to the max projection (Å) in Geometry Options the result it gives is Lenght perpendicular to the min area. should not it be max area?

regards,

Dwi

Hi Dwi

please see the attached figure.

Perhaps the easiest way to grasp the meaning of the minimal and maximal projection area of a 3d molecule is the  "biggest and the smallest possible shadow". The detailed projection figure (the shadow itself) is not drawn on the figure however the biggest circle around these two shadows are shown. Yellow for the maximal and green for the minimal projected surface.The two vectors represent the size of the molecule perpendicular the regarding plane.

We had a fruitful discussion on the field :

https://www.chemaxon.com/forum/viewpost34190.html&highlight=projected+surface+area#34190

Observations there will be integrated in a more self-explanatory "reslults" window.

Hope this helps.

Cheers,

Adrian

Hi Adrian,

Ok, I've got the idea now.

thank you for the explanation and the link also.

 

Regards,

Dwi