AMBER Archive (2008)

Subject: AMBER: Simulating peptide linkers with AMBER

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Tue Dec 02 2008 - 14:03:42 CST

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.

Thanks

Sasha

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