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.