SanDisk Membrain Software Manual de usuario descargar pdf (Pagina 17)

1 BUILDING A STRUCTURAL MODEL OF KCSA 17

crystwatD.pdb. We will use all these ﬁles to generate the corresponding PSF

and PDB ﬁles with VMD, psfgen and the buildpsf.tcl script provided in

memtut-files/01-BUILD/. The script already takes into account the informa-

tion you gather about the protonation state of ionizable residues.

13 Open the ﬁle buildpsf.tcl with a text editor. The content should look

like:

package require psfgen

topology ../top all27 prot lipid.rtf

pdbalias residue HIS HSE

pdbalias atom ILE CD1 CD

pdbalias atom HOH O OH2

pdbalias residue HOH TIP3

foreach S { A B C D } {

segment $S {

pdb seg$S.pdb

}

coordpdb seg$S.pdb $S

patch GLUP $S:71

regenerate angles dihedrals

segment WC$S {

auto none

pdb crystwat$S.pdb

}

coordpdb crystwat$S.pdb WC$S

}

segment I {

pdb pot.pdb

}

coordpdb pot.pdb I

segment WF {

auto none

pdb filtwat.pdb

}

coordpdb filtwat.pdb WF

guesscoord

writepdb kcsav.pdb

writepsf kcsav.psf

exit

14 Read the script carefully and make sure you understand each command

line. Check how we selected the protonation state of histidines and how

we used a patch to protonate Glu71.

The script builds each segment of the protein along with the crystallographic

water molecules we selected, the water molecules we placed in the selectivity

1 2 ... 12 13 14 15 16 17 18 19 20 21 22 ... 42 43

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SanDisk Membrain Software Manual de usuario Pagina 17

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