From: John Stone (
Date: Wed Aug 20 2014 - 08:34:33 CDT

You can do this from an atom selection using text commands, e.g.:
  set sel [atomselect top "not (water within 4 of yourfavoriteligand)"]
  $sel writepdb somefilename.pdb
  $sel writepsf somefilename.psf
and so on...

  John Stone

On Wed, Aug 20, 2014 at 11:29:42AM +0200, Albert wrote:
> Hello:
> I am going to delete water molecule within 4 A around a ligand. Every
> time I have to do this from GUI: save the whole system excluding 4A
> water molecules within ligand.
> I am just wondering, can we do it from command line?
> thank you very much.
> Albert

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