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
