# Load package

package require psfgen

# Load starting structures

resetpsf

readpsf membrane.psf

coordpdb membrane.pdb

readpsf leut_autopsf.psf

coordpdb leut_autopsf.pdb

# Output a combined structure

writepsf leut_mem.psf

writepdb leut_mem.pdb

# Load combined structure

mol load psf leut_mem.psf pdb leut_mem.pdb

# Delete lipid and water molecules within 1.2 A of protein

# Get segids to check

set check_sel [atomselect top “resname POPE or water”]

set check_sel_segs [lsort -unique [$check_ sel get segid]]

foreach list_seg $check_sel_segs {

# find atoms

set current_atom [atomselect top “segid $list_seg and within 1.2 of protein”]

# delete residues

set current_res [lsort -unique [$current_ atom get resid]]

foreach res $current_res {

delatom $list_seg $res

}

}

# Output modified structure

writepsf leut_mem_no_overlap.psf

writepdb leut_mem_no_overlap.pdb

# Load modified structure for viewing

mol load psf leut_mem_no_overlap.psf pdb leut_mem_no_overlap.pdb