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1 BUILDING A STRUCTURAL MODEL OF KCSA 18

ﬁlter, and potassium ions.

15 Execute the script by typing in a Unix terminal vmd -dispdev text -e

buildpsf.tcl > buildpsf.rep (if you are using Mac OS X or Windows,

type in the Tk Console window source buildpsf.tcl instead).

16 Analyze the standard output of the script by opening the ﬁle buildpsf.rep

in a text editor.

Most of the problems when building a protein model occur in the previous

step. Warning messages in buildpsf.rep can usually be ignored, but be sure

you understand the reason for the warning.

17 Use VMD to visualize and check the ﬁles kcsav.psf and kcsav.pdb gen-

erated in the previous step.

Now you have PSF and PDB ﬁles for the KcsA tetramer with ions and some

water molecules.

Using AutoPSF. VMD provides a plugin called AutoPSF which

automates the steps described above for the generation of PSF and

PDB ﬁles. While it is good that you familiarize with the details

of each step in the structure building process, AutoPSF can save

you substantial time. AutoPSF can be launched by selecting the

Extensions → Modeling → Automatic PSF Builder menu item. Use

it only if you fully understand what you are doing.

Challenge. Using an approach similar to that used for the construc-

tion of the KcsA tetramer and its PSF and PDB ﬁles, try now to

build the crystallographic unit cell containing 8 crystallographically

related molecules. Look at REMARK 290 in the 1K4C.pdb ﬁle.

1.5 Solvating the Protein (Optional)

The next step is to solvate the protein. To do this, we use Helmut Grubm¨uller’s

SOLVATE program. This program will ﬁll in any e mpty s pace inside the pore,

as wells as surround it with water. We must then delete most of it, as there

must be no water between the protein and the lipid bilayer we will embed it

in later (note that Grubm¨uller’s SOLVATE is a stand alone software, diﬀerent

than the Solvate package provided within VMD). While recommended, in the

interest of time, this section is optional.

1 First, enter solvate in a terminal window to see some information ab out

the program and to check that it is prop e rly installed.

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