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

[Justin Lemkul]

On 12/26/12 7:46 PM, Kieu Thu Nguyen wrote:
> 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 ?
>

sed is a standard *nix command, issued from the command line.

-Justin

>
> 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
>>>>>>>> --
>>>>>>>> gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at 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
>>>>>> erikm at 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 at 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-request at 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 at 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-request at gromacs.org.
>>> * Can't post? Read 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 at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================