AMBER Archive (2007)

Subject: RE: AMBER: simulating part of a molecule with homology modeling

From: Dave, Sonya (sonya.dave_at_vanderbilt.edu)
Date: Mon Feb 12 2007 - 10:50:36 CST

Thank you for your help. I think I figured it out. I should put the water box around the original molecule, as contrary to the result of vacuum simulation. Some people at my university have suggested put it around the result of vacuum simulation. But, for this situation, that was the wrong idea.
 
Sonya
 

________________________________

From: owner-amber_at_scripps.edu on behalf of Fenghui Fan
Sent: Sat 2/10/2007 10:26 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: simulating part of a molecule with homology modeling

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" <sonya.dave_at_vanderbilt.edu> 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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