Elongate conformations

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?

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

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

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

 

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.