AMBER: Simulating peptide linkers with AMBER

From: Sasha Buzko <>
Date: Tue, 02 Dec 2008 12:03:42 -0800

Hi all,
I'm trying to use AMBER to evaluate which peptide linker is best for
connecting two protein domains. But since the complete system is fairly
large, it takes a very long time to simulate. In addition,
conformational changes in other parts of the protein would influence
total energy (calculated using MM/PBSA) and can potentially affect
accuracy of the results.

I'm wondering if there is a better way to do this.. Has anyone done any
linker simulaitons? Perhaps by isolating the linker regions from the
rest of the system..
Any suggestions would be very much appreciated.



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Received on Fri Dec 05 2008 - 18:30:27 PST
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