VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 27 2011 - 08:28:46 CST

2011/1/27 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>:
> 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.

cheers,
    axel.

> $prot writepdb without-water.pdb
> $prot delete
> Regards,
> Ajasja
> 2011/1/27 ahmet yıldırım <ahmedo047_at_gmail.com>
>>
>> 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
>>
>>
>> --
>> Ahmet YILDIRIM
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.