From: Axel Kohlmeyer (
Date: Thu Jan 27 2011 - 08:08:27 CST

2011/1/27 ahmet yıldırım <>:
> Dear users,
> I want to remove all waters from the xxx.pdb file. Then, I want to save the
> pdb file (new pdb) without waters because I need to simulate without water.
> I looked at mail list but I could not find the answer I wanted.

this topic has been discussed many time.
you won't find a custom answer that just
tells you exactly what you have to type in.
if you want that, you need to hire a personal
consultant (i can send you my hourly rates,
if you are interested).

> What should I do?

a) figure out how you can safely identify the water molecules
by their names, types, residue names, index or so on.
this is very specific to the individual pdb file. VMD is very
deliberately written to be a dumb program in this respect.
_if_ - and only if - your pdb file is consistent with the usual
bio simulation conventions, then the "water" macro in VMD
might work (you will have to test it, though).

b) create an atom selection that negates that definition, e.g.
using the selection string "not water" or "not type OW HW"

c) write out a pdb file from that selection using pdbwrite

you may be able to shortcut the procedure by providing
the selection string when writing out a file from the GUI
File Save As dialog, but i don't use that, so you have to
try for yourself or look into the user's guide.

how to define and use atom selections on the VMD command
prompt is also extensively explained in the user's guide
and there are tutorials available, too.

good luck,

> Thanks in advance
> --

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.