[gmx-users] Re: gmx-users Digest, Vol 104, Issue 83
fatemeh ramezani
fr_750 at yahoo.com
Wed Dec 19 12:02:03 CET 2012
Dear Justin
I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file?
thank you
Fatemeh Ramezani
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Today's Topics:
1. merge .gro, .top files (Kieu Thu Nguyen)
2. Re: GPU running problem with GMX-4.6 beta2 (Albert)
3. Re: merge .gro, .top files (Tsjerk Wassenaar)
4. Re: merge .gro, .top files (Erik Marklund)
5. Re: merge .gro, .top files (Vedat Durmaz)
6. Re: Re: gold-S simulation (francesco oteri)
----------------------------------------------------------------------
Message: 1
Date: Tue, 18 Dec 2012 12:18:38 +0700
From: Kieu Thu Nguyen <kieuthu2212 at gmail.com>
Subject: [gmx-users] merge .gro, .top files
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CACrJSRgRHUbjqW+Zpfq=yFMcUh9OW68D2KMVkLGHeZ3ACASC2w at mail.gmail.com>
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Dear All,
I don't know which tools used to merge 2 files .gro, 2 files .top ?
Can i use trjcat ?
Thanks !
KT
------------------------------
Message: 2
Date: Tue, 18 Dec 2012 09:20:05 +0100
From: Albert <mailmd2011 at gmail.com>
Subject: Re: [gmx-users] GPU running problem with GMX-4.6 beta2
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <50D02735.9030602 at gmail.com>
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On 12/17/2012 08:06 PM, Justin Lemkul wrote:
> It seems to me that the system is simply crashing like any other that
> becomes unstable. Does the simulation run at all on plain CPU?
>
> -Justin
Thank you very much Justin, it's really helpful. I've checked that the
structure after minization and found that there is some problem with my
ligand. I regenerated the ligand toplogy with acpype, and resubmit for
mimization and NVT. Now it goes well. So probably the problems comes
from the incorrect ligand topolgy which make the system very unstable.
best
Albert
------------------------------
Message: 3
Date: Tue, 18 Dec 2012 09:30:04 +0100
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] merge .gro, .top files
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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<CABzE1SiuJhGV4O8NDjfSNu4pXTKetQmHXdi2i77vhp60NnJ8-Q at mail.gmail.com>
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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.
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
> * Please search the archive at
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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
------------------------------
Message: 4
Date: Tue, 18 Dec 2012 09:38:41 +0100
From: Erik Marklund <erikm at xray.bmc.uu.se>
Subject: Re: [gmx-users] merge .gro, .top files
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BD5228D7-229F-4E9C-9F03-66836DD50CEB at xray.bmc.uu.se>
Content-Type: text/plain; charset=us-ascii
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
>> * 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!
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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
------------------------------
Message: 5
Date: Tue, 18 Dec 2012 10:12:41 +0100
From: Vedat Durmaz <durmaz at zib.de>
Subject: Re: [gmx-users] merge .gro, .top files
To: gmx-users at gromacs.org
Message-ID: <50D03389.4030005 at zib.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
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
>>> * 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
> -----------------------------------------------
> 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
>
------------------------------
Message: 6
Date: Tue, 18 Dec 2012 10:52:17 +0100
From: francesco oteri <francesco.oteri at gmail.com>
Subject: Re: [gmx-users] Re: gold-S simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAFQcp-NrpPk_gfunfFOWnyrDVF4k6Jp4f3NGaCrFUoBx_R64Vw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear fatemeh,
in the topology file there is a section called [ bonds ] where the covalent
bonds are listed. You should add you bonds there. But I think modifing
specbonds.dat is easier because it allows pdb2gmx to do the "dirty" job :)
Anyway, f you have to simulate bond breaking, you can use Morse potential
whose parameters can directly derived by the armonic form. Morse potential
doesn't allow the bond breaking but the overall effect is very close!
I have to admit I never used but only read about Morse potential so I
cannot do practic advices!
Francesco
2012/12/17 Justin Lemkul <jalemkul at vt.edu>
>
>
> On 12/17/12 4:01 PM, fatemeh ramezani wrote:
>
>>
>>
>> Dear Justin
>>
>> According to papers, I expect gold atom interacts with the sulfur atom of
>> amino acid cysteine covalently. But in last email you said in the case of
>> protein-Au This will not be true to add these parameters
>> in topology file. Then in which file should I add the parameters
>> between gold and sulfur?
>>
>> What do you suggest? How do I define for the program that can be
>> established between these two atoms covalent bond ?
>>
>>
> Bonds do not break and form in standard MD. For that, you need QM or
> QM/MM type calculations.
>
> If there should be a bond between Cys and Au, you need to write that into
> the topology or use the specbond.dat mechanism. pdb2gmx will not create
> bonds between Au and Cys otherwise. The other modifications you have made,
> as far as I can tell, are fine.
>
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
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>
--
Cordiali saluti, Dr.Oteri Francesco
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