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? Thanks Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 13:02 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 3:46 AM, Lara Bunte wrote: > > > Hi > > that worked. I used > > trjconv -n index.ndx -f my_molecule.pdb -o output > > > After this I got an trajectory file output.xtc > > Now I have to get really a coordinate file, i.e. pdb file. I used the command > > trjconv -s -f output.xtc -o output.pdb > > > to convert it to pdb, as I read it in this tutorial: > > > http://www.mpibpc.mpg.de/groups/de_groot/compbio/p1/index.html > > But I got this error: > > Can not open file: > topol.tpr > > > I don't have a topol.tpr file. How do I got my coordinates out of this .xtc > file? > Specify a .pdb file as the output of your original command. -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
