[gmx-users] merge .gro, .top files

[Kieu Thu Nguyen]

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 <tsjerkw at 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 <kieuthu2212 at 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 <kieuthu2212 at gmail.com
> > >wrote:
> >
> > > thank all so much :-)
> > >
> > > KT
> > >
> > > On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz <durmaz at 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 <
> > kieuthu2212 at 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
> > >>>>> --
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> > >>>>>
> > >>>>>
> > >>>>
> > >>>> --
> > >>>> Tsjerk A. Wassenaar, Ph.D.
> > >>>>
> > >>>> post-doctoral researcher
> > >>>> Biocomputing Group
> > >>>> Department of Biological Sciences
> > >>>> 2500 University Drive NW
> > >>>> Calgary, AB T2N 1N4
> > >>>> Canada
> > >>>> --
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> > >>>>
> > >>> ------------------------------**-----------------
> > >>> 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
> > >>> erikm at xray.bmc.uu.se
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> > >>>
> > >>>
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
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