Re: what is the difference in force field parameters between amber6 and amber8?

hi sandhya,

I see that you have ventured into the murky world of molecular dynamics simulation. By your question you obviously have some understanding of AMBER, but here's a brief introduction for any other readers.

AMBER is a package of molecular simulation programs. When we obtain the structure of a biological macromolecule (such as a protein) using X-ray crystallography, we get a static view of the molecule - it's like a snapshot of one moment in time. In reality of course, molecules are in motion. We can't image large molecules in motion, so we rely on what's called molecular dynamics simulation. This is a complex and computationally intensive procedure. Basically, we need to calculate the forces that act one every atom in our molecule. Then, using Newton's laws of motion, we can simulate the motion of the molecule over short timescales (pico- or nanoseconds) and watch our molecule "wiggle about". This can give us an idea of how it may behave in real life, for instance when binding to a substrate.

To simplify the process, programs such as AMBER use models called force fields. The idea is that by knowing the number of atoms in the molecule, their physical properties (like charge), their bond lengths, bond energies, solvation state and so on, we can sum all of these properties and estimate what forces act on each atom.

OK, now for your specific question. AMBER actually contains a number of different force fields from which you can choose. In AMBER6 there was a default force field which in newer versions of AMBER is called "ff94". In AMBER8 there is no longer a default force field - you have to specify which one to use. This can be ff94, ff96, ff98 or a number of others.

I suggest that you visit the AMBER website and read some of the documentation which describes the force fields in each version and provides references. To get you started, the AMBER6 manual is here and some details on AMBER6 force fields is here. AMBER8 manuals are available as PDFs.

You'll notice that the current version of AMBER is 9 so if you're planning on using the software, it's generally best to go with the newest version and not worry about 6/8. And if you're really into molecular dynamics I have to put in a word for GROMACS. This is an open-source MD package and so it's freely available. It's also fast and has good support.