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Protein in a given radius water sphere

We try to solvate apomyoglobin in water sphere of radius 50$\AA$. 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.



Srinivasa Murthy .G 2004-05-02