Elongate conformations

User 8f9f7c7332

05-06-2012 00:31:00

3D optimization in MarvinSketch of molecules containing quite long and flexible chains leads to chain "globulization". Is there a way to obtain maximally elongate conformation instead?

ChemAxon d51151248d

08-06-2012 07:16:03

Dear Palek !


Can you give me an example molecule you generated the conformers for and gave the result ?


I made a rapid test with a central sp3 C with 4 sprouting C10 aliphatic chains generating 100


conformers and the lowest energy conformer respectively. The lowest energy conformer turned out


to be the "most elongated" one and "globulized" conformers had  higher energy.


So in the test case asking for the lowest energy conformation gave the "most


elongated" conformer. Maybe that would solve your problem in your case too.


 


Thanks, Daniel

User 8f9f7c7332

10-06-2012 16:31:46

I wanted to build maximally elongated molecule of an oligonucleotide, for example, containing 30 thymidines, to find out its maximal possible length.

ChemAxon d51151248d

13-06-2012 09:30:22

Dear Palek !

Unfortunately you can't elongate such an oligonucleotid in MarvinSketch
using the 3D cleaner or the conformer generator. It would need changing the
internal coordinates by hand and that's not supported.
To do that you should set the internal coordinates (e.g. torsional angles)
manually with e.g. GaussView GUI and measure the maximal possible length of
the chain. The output of Gaussian can be read by Marvin.   


Daniel


 

User 870ab5b546

13-07-2012 14:38:28

I've created a Web page that allows you to set manually the dihedral angles of a structure.  I've attached a version of the code.  I cobbled the two pages together from a bunch of separate pages, so you may need to fiddle with it a bit to get it to work. You should be able to modify it to convert all the bonds in a long chain to 180° dihedral angles.