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CONTENTS 4

Introduction

This tutorial is designed to guide users of VMD and NAMD through all the

steps required to set up a membrane protein system for molecular dynamics

simulations. The tutorial assumes that you already have a working knowledge

of VMD and NAMD. For the accompanying VMD and NAMD tutorials go to:

http://www.ks.uiuc.edu/Training/Tutorials/

This tutorial has been designed speciﬁcally for VMD 1.8.6 and NAMD 2.6 but

will also work with VMD 1.8.7 and NAMD 2.7. It should take about 5 hours

to complete in its entirety. This time can be reduced by skipping the optional

section 1.5 and by using the example scripts where provided.

The tutorial is subdivided into three separate units. The ﬁrst unit covers steps

required to set up a structural model of a membrane protein starting from a raw

PDB ﬁle. The second unit describes the steps needed to place the protein in a

native-like membrane environment. Finally, the third unit describes the steps

required to minimize and equilibrate the resulting system with NAMD.

The examples in the tutorial will focus on the study of the KcsA membrane

protein – an archetypal potassium channel with very intere sting properties.

Throughout the text, some material will be presented in separate “boxes”.

These boxes include complementary information to the tutorial, such as in-

formation about the biological role of KcsA, and tips or technical details that

can be further explored by the advanced user.

If you have any questions or comments on this tutorial, please email the TC B

Tutorial m ailing list at [email protected]. The mailing list is archived at

http://www.ks.uiuc.edu/Training/Tutorials/mailing list/tutorial-l/.

KcsA. This tutorial will focus on preparing a system that contains

the potassium channel KcsA embedded in a fully hydrated mem-

brane. KcsA was the ﬁrst ion channel crystallized; it is made of

four identical subunits forming a tetramer and features a selectivity

ﬁlter which permits highly selective conduction of potassium ions at

nearly bulk diﬀusion rates across the membrane. KcsA belongs to

a family of channels found in almost all organisms. These channels

have diverse functions and have been implicated in osmotic regula-

tion and neuronal signaling.

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