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

[Kieu Thu Nguyen]

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
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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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