Dear Tsjerk,<br><br>Thank you. Problem is solved.<br><br>Removing waters from the pdb file:<br><br>grep -v "HOH" xxx.pdb > nosol.pdb<br><br><br><div class="gmail_quote">27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hey,<br>
<br>
Well, for those things it also doesn't hurt to know a few standard linux tools:<br>
<br>
grep -v "SOL" xxx.pdb > nosol.pdb<br>
<br>
And if there are also ions in play:<br>
<br>
grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
2011/1/27 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>:<br>
<div><div></div><div class="h5">><br>
><br>
> ahmet yıldırım wrote:<br>
>><br>
>> Dear users,<br>
>><br>
>> I want to remove all waters from the xxx.pdb file. Then, I want to save<br>
>> the pdb file (new pdb) without waters because I will use the methanol as a<br>
>> solvent. I looked at mail list but I could not find the answer I wanted.<br>
>><br>
>> What should I do?<br>
>><br>
><br>
> Please read trjconv -h, with special attention to point #2 in the opening<br>
> list.<br>
><br>
> -Justin<br>
><br>
>> Thanks in advance<br>
>><br>
>> --<br>
>> Ahmet YILDIRIM<br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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<br>
<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>