AMBER Archive (2007)

Subject: AMBER: Solution Structure Determination Protocols - Simulated Annealing

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Tue Dec 04 2007 - 11:23:16 CST

Dear Amber Users,

Reading the litterature, I have noticed there are many variations
among NMR refinement protocols but the idea is the same: restratined
simulated annealing. However, when producing the final set of
structures I have noticed two main differences:

1. First start from a set of high temperature structures and then take
the lowest energy 10 - 30 structures after refinement and grouping
them into "the final set."

2 First starting from a set of high temperature structures and then
take the lowest structure (one single structure), subjecting it to
solvated MD. Then, compile an ensemble of structures from the last
portion of the solvated MD run to make the "final set."

When determining and publishing a solution structure, is one of the
above methods more prefered or more correct than the other?

Thanks,
Seth
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