VMD-L Mailing List

From: cmhartshorn (cmhartshorn_at_wsu.edu)
Date: Mon May 11 2009 - 17:31:55 CDT

Mark,
I usually use the following to select every whole water molecule in a box the size of xyz:

[atomselect top "water and same residue as (not hydrogen and (z > -33 and z < 40) and (x > -27 and x < 27) and (y > -27 and y < 27))"]

Thus, maybe this would work for you:

set water [atomselect top "water and same residue as (not hydrogen and within 3.8 of protein)"]

Hope this helps.

Best,
Chris Hartshorn
WSU

On May 11, 2009, at 10:35 AM, Mark M Huntress wrote:

I am trying to select waters near my protein, so my selection is "within 3.8 of protein" but this gives me many water atoms (lone H's and lone O's) that don't include the whole molecule, because the other atoms are outside of the 3.8 Å cutoff range. Is there a way I can select the whole water molecules and not extra atoms? I need to save a file that is realistic.
Thanks,
Mark