We try to solvate apomyoglobin in water sphere of radius 50
. Launch the vmd and then get the tkcon window by selection Extensions
tkcon inVMD Main window.
solvate myo.psf myo.pdb -o myowater -b 2.4 -t 50
mol load psf myowater.psf pdb myowater.pdb
set all [ atomselect top all]
$all set beta 0
set nonsph [ atomselect top "water and same residue as ( not hydrogen and ((x*x + y*y + z*z) > 2500))"]
$nonsph set beta 1
set badwater [ atomselect top "name OH2 and beta > 0" ]
resetpsf
readpsf myowater.psf
coordpdb myowater.pdb
foreach segid [ $badwater get segid ] resid [ $badwater get resid ] { delatom $segid $resid }
writepsf myowater50.psf
writepdb myowater50.pdb
mol delete all
mol load psf myowater50.psf pdb myowater50.pdb
The above procedure of solvation was got from here.