[gmx-users] merge .gro, .top files
durmaz at zib.de
Tue Dec 18 10:12:41 CET 2012
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
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
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.
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[-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.
>> 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 !
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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
>> gmx-users mailing list gmx-users at gromacs.org
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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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