Hi All,

I'm a computer programmer and it turns out that a piece of protein-ligand docking software (Gramm) satisfies all of the requirements I need to accomplish a certain task. The problem here being, since I'm not a molecular biologist, I think I'll require some tips on how to pull this off.

Here's what I'm doing:

I am basically trying to fit things together geometrically. Say I had a brick but the brick is now broken in half. I'm confident the software is smart enough to come up with the correct orientation of a half-brick so it fits the other half-- unbreaking the brick.

You can see where this is going... I'm planning to make PDB files that represent artificial objects.

Being only an armchair scientist, I still know enough that the software isn't designed to just match surfaces; it's designed to find a lowest Gibbs free energy state. So I don't just need to come up with fake macromolecules of the right shape, they also have to have the correct composition. After all, two halves of a brick don't just match on the surface where they broke, they also have a number of matching flat sides.

So the question is, what would that composition be? If I don't know which surfaces are the broken surfaces, should I just simulate everything as argon atoms? Or would that not allow any free energy drop at all? Or should one half-brick be oxygen atoms and the other one be hydrogens? Or just all oxygens since O2 seems to exist in nature?

If I do know which surfaces were the broken surfaces, what would be the ideal composition of the broken vs. non-broken surfaces so that the 'unbroken' orientation of the objects results in the ideal solution?

Any help would be appreciated.

Sincerely,

-Todd