From: Karteek K. Bejagam (
Date: Sun May 16 2021 - 14:15:17 CDT


I typically use, "Same residue as within 5 of selection" to select the
water molecules.

To delete them, probably use

"Not same residue as within 5 of selection "

In your case, you can also add "same residue as" so that the molecules
won't break within the selection.

Hope this helps,

On Sun, May 16, 2021, 12:50 PM Eduardo Estevez <>

> Dear VMD users
> I am trying to erase some water molecules that are too close to my protein
> and nanotube, I used the seleted Atoms option using a logical conditional
> according to the geometry of the nanotube (x² + y²> = R²) however this
> methodology cuts the molecules of water in half leaving some atoms alone
> and in the case of fibril it is very difficult for me to use this method. Please
> ask for a suggestion with some plugin or similar TCl code that allows to
> eliminate the water molecules with a specific distance.
> Sincerely
> Eduardo