#TM31C geextraheerd uit system.pdb van TM31C_popc128 (op die manier alignment met membraan al ok)

vmd -dispdev text

package require psfgen
topology ../lib/top_all27_prot_lipid_c36.rtf
segment TMP {
pdb tm31C.pdb
}
regenerate angles dihedrals
coordpdb tm31c.pdb TMP 
guesscoord
writepdb TMP.pdb
writepsf TMP.psf

(opnieuw opstarten)
package require psfgen
readpsf TMP.psf
coordpdb TMP.pdb
readpsf md100ns_124l_out.psf
coordpdb md100ns_124l_out.pdb
writepsf system_temp.psf
writepdb system_temp.pdb

#dan box groter maken
/cellsize.sh system_temp.pdb
Xmin =-0.833 Xmax =62.195
Ymin =-0.815 Ymax =65.196
Zmin =-0.831 Zmax =78.386

z dimensie groter maken naar 88
(manueel cryst info toegevoegd > system_large.pdb)

package require solvate
solvate system_temp.psf system_large.pdb -b 1.5 -minmax {{-0.1 -0.1 78} {62 65 88}}

solvate.pdb en solvate.psf gekopieerd naar work dir en hernoem in system...