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
