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

[Kieu Thu Nguyen]

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
>> http://www2.icm.uu.se/molbio/**elflab/index.html<http://www2.icm.uu.se/molbio/elflab/index.html>
>>
>>
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