Hi Justin
Thanks, that makes sense. I have the group "Close to ISO" that contains the water molecules in my specified region and I have the group ISO and therefore the next step is to unite this two groups. If I typed make_ndx -f molecule.pdb -n index.ndx -o index_new.ndx the make_ndx program shows only one group, the "Close to ISO" with number 0 and no other groups, so how to merge them? I typed l for "list residues" and than there was ISO and SOL. Now if I am at this place, how to tell GROMACS, that ISO is a group also, that I can merge it with "Close to ISO"? Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 20:55 Dienstag, 1.Mai 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 5/1/12 2:40 PM, Lara Bunte wrote: > Hi > > There is a new problem :-( > > If I used the commands > > g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 > of resname ISO' > > and > > > trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb > > I got only water in my output.pdb > As you should expect. Your command creates a group called "Close to ISO" that consists of any residue named SOL that has any atom within 1.2 nm of a residue named ISO. > Than I tried all 8 possible permutations of ISO and SOL in g_select and I > always got only water or only the molecule without any water. > > But what I need is the molecule and only three layers of water around the > molecule. > > What is the problem? > There is no problem, you just need to do a bit more work. You now have an index file with the water molecules that satisfy your criteria. You then need to utilize that index file to create a new, merged group consisting of ISO and the water molecules. You can use make_ndx: make_ndx -f molecule.pdb -n index.ndx -o index_new.ndx Type "help" to see examples. What you need to do is merge your ISO group with your "Close to ISO" group. So, for instance, if ISO is group 1 and "Close to ISO" is group 5, you would type: 1 | 5 at the make_ndx prompt, which will create a group called Close_to_ISO_ISO, thus a merged group of all atoms in "Close to ISO" and ISO. -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
