Hi I have the command
trjconv -n index.ndx -f molecule.pdb -o output.pdb that don't work because of the missing topol.tpr file. You wrote: >Supply your .pdb file to the -s flag Where exactly do I have to write -s in my command? Thanks for help Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 19:44 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 1:27 PM, Lara Bunte wrote: > 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. > Supply your .pdb file to the -s flag. Sorry for my confusion. If your desired output requires atom names, etc. you must invoke -s to read those names. An .xtc file is agnostic to all this information. Thus in your case, you need a source of atom/residue naming. A .tpr file is not strictly required for this purpose, but again, be mindful of what Gromacs expects as default input - that is why the error is coming up. Under most circumstances for trjconv operations, a .tpr file is passed to -s, but in your case, a .pdb will suffice. -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
