From davide.pirolli@rm.unicatt.it Thu Apr 22 06:58:06 2010
From: Davide Pirolli <davide.pirolli@rm.unicatt.it>
To: modeller_usage@salilab.org
Subject: [modeller_usage] (no subject)
Date: Thu, 22 Apr 2010 15:57:55 +0200
Message-ID: <56347.150.146.6.177.1271944675.squirrel@www.rm.unicatt.it>
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Hello,



<style type=3D"text/css">
	<!--
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	--></style>I'm a PhD student and I'm using modeller version 9. I'd very
glad if you could explain to me which is the solvation model used by
modeller in the various steps (in particular in the simulated annealing
refinement procedure, CG_minimization, MD etc.) and the temperatures at
which SA is carried out in the high optimization level procedure.
Many thanks in advance.
Davide Pirolli

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 messaggio
istituzionale l'Ateneo dei cattolici italiani chiede un segno di amicizia e
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Dona il Tuo "5 x mille" all'Universita' Cattolica: codice fiscale
02133120150. Info: www.unicatt.it/5permille=20
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From modeller-care@salilab.org Thu Apr 22 07:26:38 2010
From: Modeller Caretaker <modeller-care@salilab.org>
To: modeller_usage@salilab.org
Subject: Re: [modeller_usage] (no subject)
Date: Thu, 22 Apr 2010 07:26:37 -0700
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On 4/22/10 6:57 AM, Davide Pirolli wrote:
> I'm a PhD student and I'm using modeller version 9. I'd very glad if you
> could explain to me which is the solvation model used by modeller in the
> various steps (in particular in the simulated annealing refinement
> procedure, CG_minimization, MD etc.)

No solvation model is used. The effect of solvation, like 
electrostatics, is assumed to be encoded in the structure of your 
template(s), and thus in the distance restraints derived from those 
templates.

> and the temperatures at which SA is
> carried out in the high optimization level procedure.

Look at the Python functions defined in 
modlib/modeller/automodel/refine.py under your Modeller installation 
directory. They define the temperatures and other parameters for the SA 
dynamics runs.

	Ben Webb, Modeller Caretaker
-- 
modeller-care(a)salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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