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? Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 18:39 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 11:01 AM, Lara Bunte wrote: > Hi > > What do you mean with > > >> Specify a .pdb file as the output of your original command. > > I wrote in > > > trjconv -s -f output.xtc -o output.pdb > > > in the last part output.pdb. What should I specify more? > When I was referring to your "original command," I meant this one: trjconv -n index.ndx -f my_molecule.pdb -o output At this point, trjconv expects that you want an .xtc (trajectory) file, since you did not explicitly specify an extension. An .xtc file contains no information regarding atom names, so converting it back to a .pdb file requires a .tpr file, as the error you got (below) indicates. If you want to make your life simple, be more specific in what you tell trjconv. Want a .pdb file? Tell it so: trjconv -n index.ndx -f my_molecule.pdb -o output.pdb -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 -- 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
