With all due respect to people behind PISA server (which is a fantastic tool), there is probably no good answer to the crystallogrphy's question. The main contribution to the free energy of protein association is probably hydrophobic interaction, while the mentioned types of interactions are hard to quantify (salt bridges, for instance, can be both stabilizing and destabilizing depending on their environment). Remember that most of these specific interactions are substituted by corresponding interactions with solvent upon complex dissociation. There are couple of servers you can try (and plenty of literature on the subject). http://structure.pitt.edu/servers/fastcontact/ http://sparks.informatics.iupui.edu/czhang/complex.html Also remember that crystal structures do not always contain all the information needed for accurate estimates of free energies. And maybe consider a different alias :) Ed. On Thu, 2010-05-13 at 17:16 -0600, Maia Cherney wrote:

PISA server

crystallogrphy wrote:

...

Hi, I am trying to calculate the free energy of association for structure of a protein complexes based on the salt bridges, H-bonds and van der waals interaction? Does any one know how to do it?

Thanks! ------------------------------------------------------------------------

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