[AMBER] Can mm-pbsa be limited to simulating a fragment of a large protein?

From: Sasha Buzko <obuzko.ucla.edu>
Date: Fri, 11 Jun 2010 10:50:35 -0700

I'm trying to estimate the interaction energy of a rather large
protein-protein complex. Simulating the whole thing even for a few ns
would take forever..
Is it reasonable to limit the size of the simulated system to just the
neighborhood of the binding interface with, say, 15 A cutoff? And
restrain the borderline residues?
Has anyone tried this and would it still produce usable numbers?

Thanks for any suggestions


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Received on Fri Jun 11 2010 - 11:00:04 PDT
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