AMBER Archive (2008)

Subject: AMBER: how to get the potential energy of a protein from the system

From: TaoPaul (
Date: Thu Jul 31 2008 - 03:29:08 CDT

Hi, all

I am a freshman in MD. As far as I know the resulting potential energy ( "EPtot" in out file ) was that of the whole system
rather than the protein if ran a MD of protien in explicit water. So I wonder to know how
to extract the potential energy of the protein itself. Could anybody give some suggestions?

PS: my exercise is mutate some key residues in a protein, and then analyse the potentail energy difference caused by mutation.
If the EPtot is the potential energy of system, according to my understanding, the the difference of which will be less accurately than direct
difference between the protein and its mutator, isn't it?

Thanks for your help!
Best Wishes


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