On Sat, Apr 10, 2004 at 07:10:44PM +0100, Nataraj Balkrishnan wrote: > I have to add or define a new ligand to use it for modelling purpose. > In this regard I want to know.... > 1)Which liberary I have to change in modlib folder? > 2)How it should be changed(I need here some sample of small molecule that > you have changed in that liberary)?
See http://salilab.org/modeller/FAQ.html#17
> 3)Wheather we need to know all physical and chemical proterties of the > ligand(small molecule),I mean, any of those details need to be incorporated > as data inside liberary used for modeller.
You'll need to know bond, angle, and dihedral force constants. Modeller uses CHARMM parameter files for these - see www.charmm.org for more information. Such force constants are usually chosen to fit spectroscopic data or QM simulations. If you don't specify these constants, Modeller will guess them from the current atomic coordinates, which will give your ligand some flexibility.
Ben Webb, Modeller Caretaker