SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 34)

3 RUNNING A SIMULATION OF KCSA 34

3 Running a Simulation of KcsA

In unit 3, you will use the model containing KcsA embedded in a membrane to

perform molecular dynamics simulations and obtain an equilibrated system.

3.1 Melting of Lipid Tails

When using a membrane patch that has not been equilibrated, like those pro-

vided by the membrane plugin of VMD, we strongly recommend to perform

ﬁrst a simulation in which everything (water, ions, protein, lipid headgroups)

except lipid tails, is ﬁxed. In this way we will induce the appropriate disorder

of a ﬂuid-like bilayer. Here we will prepare and run such simulation.

1 Set your current directory to mem-tutorial-files/03-MINEQ/

2 Open the ﬁle kcsa popcwimineq-01.conf in a text e ditor.

We assume you are familiar with NAMD conﬁguration ﬁles (otherwise have a

look at the NAMD tutorial). However, we will discuss speciﬁc points that are

important for membrane protein simulations and for this particular simulation

of KcsA.

3 Locate the section labeled #Input. It should look like:

# Input

paraTypeCharmm on

parameters ../par_all27_prot_lipidNBFIX.prm

Note that we are not using the standard CHARMM parameter ﬁle. We are

using a parameter ﬁle that contains the so called “NBFIX” correction for the

interaction between carbonyl oxygens and potassium ions, particularly impor-

tant for the description of ions in the KcsA selectivity ﬁlter.

4 Open the ﬁle par all27 prot lipidNBFIX.prm in a text editor.

5 At the very end of the ﬁle, you should be able to ﬁnd a section labeled

NBFIX:

NBFIX

!-----Modified potassium ! Free E relative Interaction E

! to standard K+ with isolated NMA

O POT -0.1021763 3.600750 ! S.Noskov&B.Roux, 2004

O SOD -0.0750200 3.27450 ! -16.25

This section overrides the standard Lennard-Jones interactions for oxygen and

potassium ions, and for oxygen and sodium ions.

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SanDisk Membrain Software Bedienungsanleitung Seite 34