Hi In this case my problem is not solvable with gromacs?
All I have is the my_molecule.pdb which is a small molecule in a water box and my generated index.ndx file, size.xvg file and output.xtc file. Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 19:20 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 1:13 PM, Lara Bunte wrote: > Hi > If I use > > trjconv -n index.ndx -f my_molecule.pdb -o output.pdb > > I got this error again > > Can not open file: > topol.tpr > > Whats now the problem? > Apparently you need a .tpr file supplied to the -s flag to do such a transformation. I'm not sure why it's necessary in this case, but it is. -Justin -- ======================================== 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
