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? Thanks Greetings Lara ________________________________ Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> Gesendet: 23:10 Sonntag, 22.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/22/12 5:07 PM, Lara Bunte wrote: > Hi > > I got always the same error. I tried > > trjconv -n index.ndx -s molecule_in_water.pdb -o output > > Could you please send an example command how to get the coordinate file out of > my index file? > > I typed trjconv -h but I can't filter the knowledge out, thats to much for me. > You should be passing your coordinate file to -f, not -s. -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
