VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Thu Jan 27 2011 - 09:41:49 CST

well put! and Ahmet, neither remove any of your xxx files until we check
them.

2011/1/27 Axel Kohlmeyer <akohlmey_at_gmail.com>

> 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.
>
> 

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