From: Axel Kohlmeyer (
Date: Thu Jan 27 2011 - 08:28:46 CST

2011/1/27 Ajasja Ljubetič <>:
> Dear ahmet yıldırım,
> I advise you to learn some VMD/TCL scripting, but this should get you
> started:
> set prot [atomselect top "protein"]

please note,
this selection is not a good recommendation.
this assumes that the VMD macro "protein" is the
only non-water component in the system. it also
very highly depends on the .pdb file being written
according to bio-simulation conventions. _many_
codes write .pdb files that violate those and then
"protein" may not select the atoms of interest.

as i wrote before. VMD is deliberately kept dumb.
you as the user has to be smart in how to define
and tell VMD what _exactly_ you want. then VMD
in its dumb way will give you exact the desired result.

computers have no idea of common sense
or intentions. they only follow orders.


> $prot writepdb without-water.pdb
> $prot delete
> Regards,
> Ajasja
> 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.
>> What should I do?
>> Thanks in advance
>> --

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