I want to feed in a coordinates of atoms along with bond connection information. Since 
the bonding is based on some calculation I do, I need to include this information by hand. 

I tried to output the trajectory from my analysis in .mol format (following some example 
.mol file), but particles are overlapping on each other. 

Can somebody suggest me a better way to feed in coordinates and bonding information
to pymol.

Whoever fights monsters should see to it that in the
process he does not become a monster.  And when
you look into an abyss, the abyss also looks into you.
                                                 -- Friedrich Nietzsche