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 <tsje...@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 <jalem...@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 > > > > ======================================== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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