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

[Tsjerk Wassenaar]

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