VMD-L Mailing List

From: Michael LeVine (mlevine_at_wesleyan.edu)
Date: Thu Jun 17 2010 - 09:10:52 CDT

Hi,

I'm solvating a protein into a water sphere using the script supplied in the
tutorial. The script can only run until it has made the combined files, and
then gets this error:

invalid command name "HIS"
ERROR: failed while building segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

In my psfgen script I aliases HIS as HSE. Do I need to add this into the
water sphere script somewhere? Here is the script:

### Script to immerse ubiquitin in a sphere of water just large enough
### to cover it

set molname NAME

mol new ${molname}.psf
mol addfile ${molname}.pdb

### Determine the center of mass of the molecule and store the coordinates
set cen [measure center [atomselect top all] weight mass]
set x1 [lindex $cen 0]
set y1 [lindex $cen 1]
set z1 [lindex $cen 2]
set max 0

### Determine the distance of the farthest atom from the center of mass
foreach atom [[atomselect top all] get index] {
  set pos [lindex [[atomselect top "index $atom"] get {x y z}] 0]
  set x2 [lindex $pos 0]
  set y2 [lindex $pos 1]
  set z2 [lindex $pos 2]
  set dist [expr pow(($x2-$x1)*($x2-$x1) + ($y2-$y1)*($y2-$y1) +
($z2-$z1)*($z2-$z1),0.5)]
  if {$dist > $max} {set max $dist}
  }

mol delete top

### Solvate the molecule in a water box with enough padding (15 A).
### One could alternatively align the molecule such that the vector
### from the center of mass to the farthest atom is aligned with an axis,
### and then use no padding
package require solvate
solvate ${molname}.psf ${molname}.pdb -t 15 -o del_water

resetpsf
package require psfgen
mol new del_water.psf
mol addfile del_water.pdb
readpsf del_water.psf
coordpdb del_water.pdb

### Determine which water molecules need to be deleted and use a for loop
### to delete them
set wat [atomselect top "same residue as {water and ((x-$x1)*(x-$x1) +
(y-$y1)*(y-$y1) + (z-$z1)*(z-$z1))<($max*$max)}"]
set del [atomselect top "water and not same residue as {water and
((x-$x1)*(x-$x1) + (y-$y1)*(y-$y1) + (z-$z1)*(z-$z1))<($max*$max)}"]
set seg [$del get segid]
set res [$del get resid]
set name [$del get name]
for {set i 0} {$i < [llength $seg]} {incr i} {
  delatom [lindex $seg $i] [lindex $res $i] [lindex $name $i]
  }
writepsf ${molname}_ws.psf
writepdb ${molname}_ws.pdb

mol delete top

mol new ${molname}_ws.psf
mol addfile ${molname}_ws.pdb
puts "CENTER OF MASS OF SPHERE IS: [measure center [atomselect top all]
weight mass]"
puts "RADIUS OF SPHERE IS: $max"
mol delete top

Is the problem somewhere in the step where it deletes the waters? In VMD, I
got a PDB file with the protein hanging out a water box. Hopefully you can
help, thanks!

Mike