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...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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 

-- 
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/