Hi KT, To update the number of atoms in a merged .gro file, assuming a single frame and no empty lines after the box definition, you have to replace the second line with the number of lines minus three:
sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro > out.gro Cheers, Tsjerk On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > But i don't see file "gromacs_topology_merger.py" in the web Vedat gave me. > > Tsjerk, can you give me the script for updating the number of atoms ? I > searched in google, but i have not found it yet. It's really my stupid > question, but i don't know why. > > Thanks ! > Best regards, > > KT > > > On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen <kieuthu2...@gmail.com > >wrote: > > > thank all so much :-) > > > > KT > > > > On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz <dur...@zib.de> wrote: > > > >> there's also an executable topology merger available written in python > >> called "gromacs_topology_merger.py" as part of a the software package > >> "ZIBMolPy" designed for conformational analysis at > >> > >> https://github.com/CMD-at-ZIB/**ZIBMolPy< > https://github.com/CMD-at-ZIB/ZIBMolPy> > >> > >> given (in the same directory) a topology file "topol.top" (argument 1) > >> and two (or more) itp files "mol1.itp" and "mol2.itp" included in the > top > >> file, the tool writes out a new topology file (argument 2) merging the > >> first two molecules from the include sequence of which itp files are > given. > >> > >> note: the number of molecules to be merged should be 1 in the [ > molecules > >> ] section. if one of them is meant to appear multiple times in the > merged > >> topology, the process needs to be repeated accordingly. > >> > >> vedat > >> > >> > >> Am 18.12.2012 09:38, schrieb Erik Marklund: > >> > >> 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: > >>> > >>> Hi KT, > >>>> > >>>> If you mean concatenating frames in .gro files, you can use trjcat or > >>>> just > >>>> cat. If you mean merging the coordinates, it's a wee bit more > >>>> complicated. > >>>> Since you also ask for top files, I guess that's the case. Here's a > >>>> snippet > >>>> of python code that will do the trick: > >>>> > >>>> #!/usr/bin/env python > >>>> > >>>> import sys > >>>> > >>>> f = [open(i).readlines() for i in sys.argv[1:]] > >>>> print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f)) > >>>> print "".join(["".join(i[2:-1]) for i in f]), > >>>> print f[0][-1] > >>>> > >>>> > >>>> For the top files, it is necessary to ensure all the moleculetypes are > >>>> #included, and that the [ molecules ] listing under [ system ] has the > >>>> right number and order of the molecules in the merged gro file. > There's > >>>> no > >>>> tool for that that I know of. > >>>> > >>> In principle you could use grompp for checking that. It would print out > >>> a heap of warinngs/notes/errors if structure file and topology don't > match. > >>> > >>> Erik > >>> > >>> Cheers, > >>>> > >>>> Tsjerk > >>>> > >>>> > >>>> On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen < > kieuthu2...@gmail.com > >>>> >wrote: > >>>> > >>>> Dear All, > >>>>> > >>>>> I don't know which tools used to merge 2 files .gro, 2 files .top ? > >>>>> Can i use trjcat ? > >>>>> > >>>>> Thanks ! > >>>>> KT > >>>>> -- > >>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>>>> * Please search the archive at > >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search< > 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< > http://www.gromacs.org/Support/Mailing_Lists> > >>>>> > >>>>> > >>>> > >>>> -- > >>>> Tsjerk A. Wassenaar, Ph.D. > >>>> > >>>> post-doctoral researcher > >>>> Biocomputing Group > >>>> Department of Biological Sciences > >>>> 2500 University Drive NW > >>>> Calgary, AB T2N 1N4 > >>>> Canada > >>>> -- > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>>> * Please search the archive at http://www.gromacs.org/** > >>>> Support/Mailing_Lists/Search< > 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< > http://www.gromacs.org/Support/Mailing_Lists> > >>>> > >>> ------------------------------**----------------- > >>> Erik Marklund, PhD > >>> Dept. of Cell and Molecular Biology, Uppsala University. > >>> Husargatan 3, Box 596, 75124 Uppsala, Sweden > >>> phone: +46 18 471 6688 fax: +46 18 511 755 > >>> er...@xray.bmc.uu.se > >>> http://www2.icm.uu.se/molbio/**elflab/index.html< > http://www2.icm.uu.se/molbio/elflab/index.html> > >>> > >>> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >> * Please search the archive at http://www.gromacs.org/** > >> Support/Mailing_Lists/Search< > 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< > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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. 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