VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 27 2004 - 15:27:01 CDT

Here's a script-oriented example from the VMD User's Guide:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node177.html

The selection text used is:
  water and same residue as (within 2 of protein)

Here's a script that uses it:

set sel [atomselect top "water and same residue as (within 2 of protein)"]
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
  $sel frame $i
  $sel update
  $sel writepdb water_$i.pdb
}

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 24, 2004 at 01:44:57AM -0700, Sekwan Oh wrote:
> Hi,
>
> There is one polypeptide molecule solvated with water molecules.
>
> I would like to select the water molecules only within certain distance
> from the polypeptide.
>
> I found that we can use 'within' command, but I couldn't make it.
>
> The manual says it can be done by the command "within <distance> of
> <molecules>", however it's not clear for me when this command should be
> used.
>
> Could someone tell me how to do this? (e.g. What should be done first,
> seconde and so on)
>
>
> Thank you.
>
> Regards,
>
> Sekwan
>
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NIH Resource for Macromolecular Modeling and Bioinformatics
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