From: Ashar Malik (
Date: Wed Oct 29 2014 - 03:54:03 CDT


Since you need to do this on a pdb file what you need to do is to ascertain
The minimum and maximum of all bounding dimensions ... I.e. x, y and z
which mark the boundary inside the tube. Once you have that .. A simple
script can look across the coordinate section of the pdb and spit out the
residue numbers that are within the tube. Once you have those numbers you
just need to plug those into vmd's selection ... And delete. You could
delete it in the pdb with the code that finds those with the atoms in the
x,y and z, but that might disturb the atom numbering ... So best to do it
this way. When you would delete the atoms/residues falling within the tube
and right out the pdb ...VMD would automatically take care of the numbering
for you.

Dear Ajajsa,

Thanks for the reply. However, I wish to eliminate ONLY the waters inside,
and not disturb those outside.

So, assuming my nanotube axis coincides with the X-axis, I wish to
eliminate waters that fulfill the condition: r^2 < (y^2 + z^2).
Do you know how to put this selection in VMD?

Thank you.


On Tue, Oct 28, 2014 at 11:39 PM, Richard Wood <>

> Open the file in a text editor and delete them by hand once you know
> which ones they are?
> Richard
> ------------------------------
> *From:* [] on behalf of
> Asis Jana []
> *Sent:* Tuesday, October 28, 2014 11:19 AM
> *To:*
> *Subject:* vmd-l: removing water inside the nanotube
> Dear VMD experts,
> I have a solvated box with a cylindrical nanotube. I wish to remove
> waters from inside the tube.Can you suggest to me how to do this?
> Thank you.
> Asis