SanDisk Membrain Software Uživatelský manuál stáhnout pdf (Strana 19)

1 BUILDING A STRUCTURAL MODEL OF KCSA 19

Figure 5: Snapshot of KcsA’s selectivity ﬁlter obtained using ﬁles kcsav.psf

and kcsav.pdb. Note the presence of hydrogen atoms and selected potassium

ions, as well as crystallographic water molecules.

2 Now we will run Solvate on the PDB ﬁle you just produced. Type the

following command in a terminal window:

solvate -t 3 -n 8 -w kcsav solkcsa

The options provided have the following meanings:

Option Meaning

-t 3 Make the water layer 3

A thick

-n 8 Use 8 gaussians for solvent boundary

-w Output water molecules only

Also notice that we must leave the suﬃx .pdb oﬀ of the ﬁle names. This

program m ay take a few minutes to run.

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SanDisk Membrain Software Uživatelský manuál Strana 19