Dielectric constant for MDFF of a membrane protein.

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Fri Mar 30 2012 - 09:18:22 CDT

Dear NAMD users

I´m triyinf to perform a MDFF of a membrane channel protein using an
available Cryo-EM density map. Everything seems quite straightforward
from the NAMD-MDFF tutorial, but there is something that is not so
easy to define. In the typical MDFF procedure a dielectric constant
must be set to represent the solvent, and thus for water soluble
proteins this value is 80...But in the case of a transmembrane
channel, should I use a membrane like dielectric (i.e 4-6)?? or should
I start by using 80 but keeping secondary stricture highly restrained?


Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.

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