Re: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin

From: francesco oteri (
Date: Mon Feb 18 2013 - 11:31:09 CST

Hi Izhar,
are you sure that POPC is the right lipid. You could try some other lipid
whose tickness is compatible with the your channel.
It is likely that in the living cell you protein environment is not
composed by simple POPC. You should check literature to
account for such a problem.


2013/2/18 Izhar Karbat <>

> Dear NAMD users,
> I am simulating a membrane system containing an ion channel embedded in a
> POPC bilayer. The hydrophobic thickness of the ion channel (according to
> the OPM database) is 27A. The membrane patch, generated with the
> membrane-builder plugin has hydrophobic thickness of ca. 31A. As a result,
> several extracellular segments of the channel which are expected to be
> solvent exposed, are facing a lipid. While this does not seem to affect the
> simulation stability over a few ns period, i'm afraid that longer runs
> might get skewed by the imperfect placement of the membrane. As quite
> several membrane proteins deviate from the "canonic" hydrophobic thickness
> of ~30A, and since the membrane plugin does not offer control over the
> bilayer thickness,
> i hope that one of you might have encountered a similar problem in the
> past and may share is ideas concerning possible solutions.
> yours,
> Izhar.

Cordiali saluti, Dr.Oteri Francesco

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