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1 BUILDING A STRUCTURAL MODEL OF KCSA 20

3 Now we will combine the output PDB ﬁle solkcsa.pdb with the rest of

the system. Do this by entering:

vmd -dispdev text -e make solv.tcl

(or type in the Tk Console source make solv.tcl).

The content of the script is:

set sol infile solkcsa.pdb

set kcsa inbase kcsav

set outbase kcsav solv raw

package require psfgen

resetpsf

topology ../top all27 prot lipid.rtf

segment SOLV {

auto none

first NONE

last NONE

pdb $sol infile

}

coordpdb $sol infile SOLV

readpsf ${kcsa inbase}.psf

coordpdb ${kcsa inbase}.pdb

writepdb ${outbase}.pdb

writepsf ${outbase}.psf

exit

This creates the corresponding segment for the new water molecules, com-

bining them with your previous psf and pdb ﬁles.

Now we will remove unwanted water molecules, which basically means ﬁnding

good selection criteria in VMD. Here, we want to eliminate water molecules

located in the hydrophobic protein-membrane interface (Fig. 6).

Membrane-protein matching. Placement of a protein in the mem-

brane can be guided by the hydrophobicity of its residues. In cases

like KcsA, by simply looking at the protein one can get an idea of

where the hydrophobic region of the membrane will be located.

The “Orientations of Proteins in Membranes (OPM)” database

(http://opm.phar.umich.edu/) and the program “Membrane Pro-

tein Explorer” (MPEx, http://blanco.biomol.uci.edu/mpex) provide

a more rigorous way, based on energetics and thermodynamics prop-

erties, to determine which protein domains are embedded in the

membrane.

4 To make selection easier, we will ﬁrst center everything on the origin. Open

VMD and be sure that you are in the mem-tutorial-files/01-BUILD/

directory.

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SanDisk Membrain Software Manual do Utilizador Página 20