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
