VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
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...
On Wed, Aug 20, 2014 at 11:29:42AM +0200, Albert wrote:
> 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.
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/