Adventures in Computational Chemistry

I have a system with four molecules and the initial challange is to generate a combined PDB file for the four molecules together which is compatible with the AMBER software. Apparently it is a simple problem.  But here it is a problem because pdb version of molecules generated using different build up softwares find compatibility issue with Amber. Also I found very rare examples where people are trying to study multicomponent system using Amber. In other words even the Amber mailing list (http://archive.ambermd.org/) was not very helpful in solving the problem. I tried many different possibilities. I used different tutorials for Amber, but none of them were direct solutions. I finally created my own procedure understanding these tutorials and combining them together. In coming few I will try to explain how you can generate amber compatible PDB file for multi component system