Re: [AMBER] Generation of melting curves

From: Daniel Roe <>
Date: Mon, 7 Oct 2013 08:39:04 -0600


On Sun, Oct 6, 2013 at 9:59 PM, Gargi Borgohai <> wrote:
> Will you please confirm me whether I can use the population of native structure
> obtained directly from cluster structure analysis for generation of
> melting curves or not.

You *can* use cluster population, but as you have found it can be
problematic depending on how well-defined your clusters are. It's not
clear what "high" and "low" RMSD are for you, but if your "native"
cluster (I assume you're assigning this based on similarity of the
cluster representatives to a well-defined native structure) contains
non-native structures you may need to adjust epsilon in addition to
the number of clusters.

Keep in mind as well there are other ways to define what is "native"
(e.g. you could use native contacts or hbonds), and each may result in
different looking melting curves. Depending on what your ultimate goal
is, other metrics may be appropriate. For example, if you're comparing
to a melting curve obtained via CD, using a native metric based on
secondary structure content may be more appropriate.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Oct 07 2013 - 08:00:03 PDT
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