Working with a multicomponent system

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

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Adventures in Computational Chemistry

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