[gmx-users] remove all waters from the pdb file

[ahmet yıldırım]

Dear Tsjerk,

Thank you. Problem is solved.

Removing waters from the pdb file:

grep -v "HOH" xxx.pdb > nosol.pdb


27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar <tsjerkw at gmail.com> yazdı:

> Hey,
>
> Well, for those things it also doesn't hurt to know a few standard linux
> tools:
>
> grep -v "SOL" xxx.pdb > nosol.pdb
>
> And if there are also ions in play:
>
> grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb
>
> Hope it helps,
>
> Tsjerk
>
> 2011/1/27 Justin A. Lemkul <jalemkul at vt.edu>:
> >
> >
> > ahmet yıldırım wrote:
> >>
> >> 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 will use the methanol as
> a
> >> solvent. I looked at mail list but I could not find the answer I wanted.
> >>
> >> What should I do?
> >>
> >
> > Please read trjconv -h, with special attention to point #2 in the opening
> > list.
> >
> > -Justin
> >
> >> Thanks in advance
> >>
> >> --
> >> Ahmet YILDIRIM
> >>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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>



-- 
Ahmet YILDIRIM
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