AMBER Archive (2008)

Subject: AMBER: Restricting the system to simulate

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 17 2008 - 11:00:50 CDT

My task is to carry out MD (Amber 10) of a big protein-small ligand
complex by restricting the simulation to the ligand and helices
directly involved in forming the complex, and little more than that.

I find uneasy to imagine how to prune the protein. If the unwanted big
part is suppressed, the helices involved in complexing would remain
disconnected from one another. Isolated in the space.

I assume that restraining the protein not involved in complexing would
have scarce effect in shortening the MD simulation. If correct, is
there any way to make so that the unwanted part of the protein is not
involved in the simulation, as if it had been deleted? Thus only
serving as a lock.

The simulation is particularly expensive as the region of the complex
has to be immersed into a quasi-real transmembrane.

Thanks

francesco pietra
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