Re: AMBER: simulating part of a molecule with homology modeling

From: Fenghui Fan <>
Date: Sat, 10 Feb 2007 20:26:41 -0800 (PST)

I think your methods are correct. If I select, I will
select the explicit water method, and the structure
should be a random coil.

In the tutorial, there is a tutorial on structure
prediction from sequence to 3-D structure. Maybe you
can try this.

Best regards.

Fenghui Fan

--- "Dave, Sonya" <> wrote:

> Hi,
> I have a protein with unknown structure (clh3a), and
> a evolutionarily related homolog(clc0). They share a
> good deal of sequence homology in one domain that I
> am interested in (the second cbs domain). However, I
> only need the model of the last alpha helix of the
> cbs domain of clh3a. This last alpha helix shows no
> sequence homology with it's corresponding part of
> clc 0. In any case, I "aligned" the alpha and found
> a homologous structure in InsightII.
> Then, i ran the simulation of them in amber. I did
> as similar to the tutorial, first in vacuum, then
> add explicit water molecules. The vacuum simulation
> looks basically like the original alpha helix of
> clc0. However, the model using conjugate, and then
> the explicit solvents, do not show a alpha helix
> form. they just show an unstructured segment of
> amino acids. I am using the force field ff99,
> which, as I understand, emphasizes alpha helixes.
> Any suggestions? Is this the right way of
> approaching the problem? Also, does anyone know how
> I can find a homolog with more sequence homology,
> preferably something that is also part of a cbs
> domain. I tried the compartive mo deling linked
> through pubmed. However, my alpha helix is too short
> a segment for it to find a homolog (it is 7 a.a.'s)

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Received on Sun Feb 11 2007 - 06:07:53 PST
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