Re: How many ATP molecules are there in a bacterial cell?

Well, there is really now way of knowing at the current time. Even an estimate is impossible. 
Becasue to answer this question you need to know several things. They are:

1) What group of microbes are you studying?
2) What environment is it in?
3) What mode of respiration is it currently undergoing (i.e. aerobic, anerobic, etc..)?
4) What is it you want to model using ATP?

Since, I have some knowledge of what you are trying to do (I just took a class in mathematical 
modeling in molecular and systems biology) you can make it easy on your self buy looking at the 
pathways. Actually, you cant do what you are doing from a network perspective unless you know 
the molar ratios of the pathways under study. So, knowing that amount of ATP in a cell is not 
going to help you anyway. You need to know what is going on in order to do the modeling you wish 
to do. 

I suggest that you get the following books to help you on your way:
- Any Biochemistry book (e.g., Stryer or Lehninger)
      So, you can look at chemical pathways, and rates of reactions (which will effect your model)
- Random Walks in Biology by Howard Berg
- Bioprocess Engineering Basic Concepts by Shuler and Kargi
- Introduction to Operations Research by Hillier and Lieberman
- Metabolic Engineering edited by Sang Yup Lee and Eleftherios T. Papoustsakis
      This book is most likely the one you want to read through as it covers areas you seem to be 
interested in.