Re: obtaining vanderwalls volume and surface area using mol2

Hi,

      I am using Marvin Sketch version 6.3.0. I wanted to calculate Vander walls volume and surface area of molecules using this. so i have converted an X-ray structure .cif file to the allowed .mol2 file format and inserted into the software. However when i clicked on the geometrical descriptors which gives the vanderwalls volume it gives an error. same is the case with surface area. I have a large number of molecules for which i need to do this calculation hence inserting them as .mol2 file would be a better option for me. However it doesn't seems to work.

It would be helpful if you can find a solution to this problem. I am attaching the .mol2 file of the molecule for which i was trying to find the volume and surface area for your perusal.

thank you,

rajesh.

Hi Rajesh,

The attached file contains bond definition lines like this:

2     1     6   un

These bonds have undefined order therefore the structure is considered as a query structure. If you change the bond orders to have regular orders, the calculation will run. Allowed bond types are: 1, 2, 3 and aromatic.

I've attached the structure with the fixes. I guessed the bond types based on the angles and Hydrogen counts.

Regards,

Peter

2     1     6   un

Hi peter,

                  Thank you for the solution. You have mentioned that you have guessed the bond types based on hydrogen counts and angles. Can you please elaborate on this so that i can rectify the problem in case it arises for other molecules during calculation.

thank you,

rajesh.

Hi Rajesh,

The structure contained two 6-membered ring of carbon atoms with one explicit Hydrogens on them. These must be benzene rings, so I've put aromatic bonds into the rings. I could've put alternating single and double bonds too, it would have the same meaning.

The bonds attached to the benzene rings are single, the Carbon atoms in the benzene rings can connect only with single bonds outside the rings.

The other branch which have 3 bonds in a straight line must have a triple bond in it -  that's causing the 180 degree angle between the atoms. So the middle bond in the branch is a triple bond and the other one is a single.

There is only one any bond left, it can be a single or a double. Yesterday, I draw it as single bond, but today I feel more like it's a double.  If it would be a single bond, there would be more explicit Hydrogen atoms around the Carbon atoms.

It's generally a good hint to turn on all Implicit Hydrogen atoms in the View menu and try to add bonds that doesn't cause valence errors but makes the implicit Hydrogen atoms disappear. This is not a 100% sure method, you may try to compare the resulting structure with the one in the .cif file in an other program.

I hope it's more clear for you now. I attached the structure with the double bond.

Regards,

Peter