Re: ABF Method

From: digenova (digenova_at_gmail.com)
Date: Thu Jul 03 2008 - 08:52:29 CDT

use z-coord as reaction coordinate. maybe you don't see move leucine
because the distance between abf1 and abf2 is 0.
El mié, 02-07-2008 a las 10:19 -0400, Bonnie A Merchant escribió:
> I am currently studying the transport mechanism of leucine through the
> leucine transporter. I have been using the ABF method and
> distance-com. Once the leucine moves half-way through from the
> extracellualar side to the binding pocket, it appears to stop and will
> not move any further. Even when using stronger forces, it will not
> proceed through the rest of the trasnporter.
>
> Does anyone have any suggestions? Should be be using Zcoord?
>
>
>
>
> Bonnie Merchant
> merchantba_at_carlow.edu
>
>

-- 
Alex Di Genova Bravo.
Ingeniero en Bioinformatica.
Lab. de Bioinformatica y Matematica del Genoma
Centro de Modelamiento Matematico
Fac de Cs Físicas y Matematicas, Universidad de Chile
Av. Blanco Encalada 2120, Piso 6.

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