From: Leonhard Henkes (
Date: Wed Jun 25 2008 - 07:31:10 CDT

Dear VMD user,
at the moment I have set up a box system (x=50 Angstrom , y= 50 Angstrom, z=100 Angstrom) including water, a lipid bilayer (POPE) and a protein placed in the middle. The problem are some water molecules around the membrane. After reading the psfgen User Guide 1.4.5. I tried to reproduce the script for "deleting unwanted atoms" in which they produce a box and delete all the water outside the box. I liked the idea of deleting water with a box and I started to modify the script in a way, that it should delete all the waters inside this box/area. In the end, all waters get deleted and I'm running out of ideas, so plz have a look at my script and help me out.

Thx for all your help,

source "Config_leo.tcl"
package require psfgen
topology top_all27_prot_lipid.inp

readpsf $input.psf
coordpdb $input.pdb
mol load psf $input.psf pdb input.pdb

set water_del [atomselect top "name OH2 and (x<25 or x>-25 or y<25 or y>-25 or z <25 or z>-25)"]
foreach segid [$water_del get segid] resid [$water_del get resid] {
  delatom $segid $resid

writepdb $TEST_water.pdb
writepsf $TEST_water.psf


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