[gmx-users] remove all waters from the pdb file
tsjerkw at gmail.com
Thu Jan 27 20:37:32 CET 2011
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,
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
>> 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
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Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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