Do you mean that i have to add the line "sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro > out.gro" into the old script merge.py ?
On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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. 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