VMD-L Mailing List

From: srinivasa murthy (srim729_at_yahoo.co.in)
Date: Tue Sep 23 2003 - 01:40:10 CDT

hi,
   I am new user of VMD. I am using vmd-1.8.1(binary
for linux). I wanted to create a water sphere of
radius 10 angstrom . I went
through vmd-l mailing list and found tcl script for
the purpose(Re: creating spherical water
droplet->Justin Gullingsrud ).Script goes like this(i
have modified slightly..though original one gave same
result)

package require psfgen
set rad 10
set r2 [expr $rad*$rad]
set wat2delete [atomselect top
"(sqr(x)+sqr(y)+sqr(z)>$r2"]
foreach segid [$wat2delete get segid] resid
[$wat2delete get resid] {
  delatom $segid $resid
}
writepsf watsph.psf
writepdb watsph.pdb

I ran this script after creating a water box using
solvate -o new -minmax { { 0 0 0} {50 50 50} }
and loading new.pdb and new.psf to vmd..

I get this output in vmd Tkcon console after the
foreach loop
no segment WT1
no segment WT1
..
..
..
or if i use only resid in foreach loop
no segment 4
no segment 4
..
..
no segment 250
no segment 250
..
..

but when i use $wat2delete get resid .. i got the list
of water molecules to be deleted..

what could be the problem

regards
srinivasa

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