NeonCortex - 24-10-2007 at 04:52
I have just started to use Chem3D and am familiarizing myself with the functions. I encountered a thing I would like some help with. It concerns doing
structure overlays to compare structures and conformations. As an example I'll be using Tapentadol and Morphine.
First I select the phenolic OH of each molecule, the sidechain and nitrogen of tapentadol and a similar sidechain and nitrogen in morphine. Then I'd
like to overlay these atoms with the optimal distance 0, up to this point everything is OK. I'd like each molecule to minimize energy independently of
each other and that the rest of the molecule and conformations minimize. Basically I want to anchor some atoms and the rest to minimize. Chem3D seems
to keep the conformations already arranged.
If anyone know how to introduce solvent and ionic strength into the calculations, that would be much appreciated also.
vulture - 24-10-2007 at 07:59
You can choose to only minimize selected atoms. A solvent selection is possible for certain calculation methods, but I doubt it is for ionic strength.
You're aiming for simulations of the kind that gaussian does. Be prepared to spend a few days calculating on that with a modern PC.
NeonCortex - 24-10-2007 at 12:13
Ahhh, easier than I thought then. Thank you very much!