[gmx-users] problems with martinize.py
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 20 16:54:23 CET 2012
francesca vitalini wrote:
> Thanks Tsjerk, Florian,
> However I need the .gro file for the reverse transformation and I
> cannot simply obtain it through pdb2gmx as it won't recognize the
> atoms
>
Use editconf to convert between .pdb and .gro (as well as other formats).
pdb2gmx is for producing topologies, not interconverting coordinate files.
-Justin
> Fatal error:
> Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms
> while sorting atoms.
> .
>
> Any help with that?
> Thanks a lot
>
>
>
> 2012/2/20 Dommert Florian <dommert at icp.uni-stuttgart.de>:
>> On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote:
>>> Just one last question Tsjerk, I was trying to load the cg.gro file
>>> obtained with martinize in vmd and the program says it is unable to
>>> load the molecule. the result of the martinize script looks like:
>>>
>>> MODEL 1
>>> TITLE Protein in water
>>> CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1
>>> ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00
>>> ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00
>>> ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00
>>> TER
>>> ENDMDL
>>>
>> This looks like a PDB file. If you load cg.gro into VMD it will
>> recognize it as GRO file, but you provide the wrong format. Rename
>> cg.gro to cg.pdb and it should be loaded successfully into VMD.
>>
>> /Flo
>>
>>> Does it sound right to you?
>>> Thanks
>>>
>>>
>>>
>>> 2012/2/20 francesca vitalini <francesca.vitalini11 at gmail.com>:
>>>> Thank you so much.. Now it is working. I was trying to do it without
>>>> specifying the secondary structure as I'm having problems with the
>>>> do_dssp command. It is not working basically and I have to use pdb2gmx
>>>> to convert into pdb then go to the dssp webpage and create the dssp
>>>> file from there through the pdb. Do you know a fastest way to make it
>>>> work? Thanks
>>>>
>>>> However, my Martini account never worked, don't know why, so I cannot
>>>> post it directly.
>>>>
>>>> 2012/2/20 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>>>>> Hey Francesca,
>>>>>
>>>>> Now there's a small bug in the program. Sorry about it. We'll put the
>>>>> fixed version on in a bit. The problem arises because you don't
>>>>> specify the secondary structure and pymol is not yet available for
>>>>> doing so. The workaround is to explicitly set the secondary structure
>>>>> to loop, by adding "-ss LLL" on the command line. Thanks for pointing
>>>>> that out.
>>>>>
>>>>> By the way, you might want to post these issues on the Martini forum:
>>>>> http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum
>>>>> It's not exactly Gromacs...
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Tsjerk
>>>>>
>>>>> On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini
>>>>> <francesca.vitalini11 at gmail.com> wrote:
>>>>>> Done while waiting for your e-mail. the error message now says
>>>>>>
>>>>>> INFO Chain termini will be charged
>>>>>> INFO Residues at chain brakes will not be charged
>>>>>> INFO Local elastic bonds will be used for extended regions.
>>>>>> INFO Position restraints will be generated.
>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in
>>>>>> the MDP file
>>>>>> INFO Read input structure from file.
>>>>>> INFO Input structure is a PDB file.
>>>>>> INFO Found 1 chains:
>>>>>> INFO 1: (Protein), 25 atoms in 3 residues.
>>>>>> INFO Total size of the system: 3 residues.
>>>>>> Traceback (most recent call last):
>>>>>> File "./martinize-1.0.py", line 2415, in <module>
>>>>>> elif options["-pymol"]:
>>>>>> KeyError: '-pymol'
>>>>>>
>>>>>> and the pdb looks like
>>>>>>
>>>>>> TITLE Protein in water
>>>>>> REMARK THIS IS A SIMULATION BOX
>>>>>> CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1
>>>>>> MODEL 1
>>>>>> ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00
>>>>>> ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00
>>>>>> ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00
>>>>>> ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00
>>>>>> ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00
>>>>>> ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00
>>>>>> ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00
>>>>>> ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00
>>>>>> ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00
>>>>>> ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00
>>>>>> ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00
>>>>>> ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00
>>>>>> ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00
>>>>>> ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00
>>>>>> ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00
>>>>>> ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00
>>>>>> ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00
>>>>>> ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00
>>>>>> ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00
>>>>>> ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00
>>>>>> ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00
>>>>>> ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00
>>>>>> ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00
>>>>>> ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00
>>>>>> ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00
>>>>>> TER
>>>>>>
>>>>>>
>>>>>> can you please explain which the problem is to me?
>>>>>>
>>>>>> thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2012/2/20 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>>>>>>> Hi Francesca,
>>>>>>>
>>>>>>> Given the error, it seems there's still a mismatch between the number
>>>>>>> of atoms and the number indicated. Try converting your structure to
>>>>>>> PDB and use that for coarsegraining.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Tsjerk
>>>>>>>
>>>>>>> On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini
>>>>>>> <francesca.vitalini11 at gmail.com> wrote:
>>>>>>>> I've changed that but it is still complaining...
>>>>>>>>
>>>>>>>> INFO Chain termini will be charged
>>>>>>>> INFO Residues at chain brakes will not be charged
>>>>>>>> INFO Local elastic bonds will be used for extended regions.
>>>>>>>> INFO Position restraints will be generated.
>>>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in
>>>>>>>> the MDP file
>>>>>>>> INFO Read input structure from file.
>>>>>>>> INFO Input structure is a GRO file. Chains will be labeled consecutively.
>>>>>>>> Traceback (most recent call last):
>>>>>>>> File "./martinize-1.0.py", line 2306, in <module>
>>>>>>>> for title,atoms,box in frameIterator(inStream):
>>>>>>>> File "./martinize-1.0.py", line 1183, in groFrameIterator
>>>>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
>>>>>>>> File "./martinize-1.0.py", line 1170, in groAtom
>>>>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
>>>>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
>>>>>>>> ValueError: invalid literal for int() with base 10: '2.'
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2012/2/20 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>>>>>>>>> Hi Francesca,
>>>>>>>>>
>>>>>>>>> The problem is that the second line of your gro file indicates there
>>>>>>>>> are 2410 atoms in the file, while there are only 25. Did you manually
>>>>>>>>> remove water? In that case you have to update the number of atoms in
>>>>>>>>> the second line. The error message should be more explanatory though.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>> Tsjerk
>>>>>>>>>
>>>>>>>>> On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini
>>>>>>>>> <francesca.vitalini11 at gmail.com> wrote:
>>>>>>>>>> I was using the one available from the tutorial but now I have
>>>>>>>>>> downloaded the new one and it gives me still an error message like
>>>>>>>>>>
>>>>>>>>>> INFO Chain termini will be charged
>>>>>>>>>> INFO Residues at chain brakes will not be charged
>>>>>>>>>> INFO Local elastic bonds will be used for extended regions.
>>>>>>>>>> INFO Position restraints will be generated.
>>>>>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in
>>>>>>>>>> the MDP file
>>>>>>>>>> INFO Read input structure from file.
>>>>>>>>>> INFO Input structure is a GRO file. Chains will be labeled consecutively.
>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>> File "./martinize-1.0.py", line 2306, in <module>
>>>>>>>>>> for title,atoms,box in frameIterator(inStream):
>>>>>>>>>> File "./martinize-1.0.py", line 1183, in groFrameIterator
>>>>>>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
>>>>>>>>>> File "./martinize-1.0.py", line 1170, in groAtom
>>>>>>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
>>>>>>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
>>>>>>>>>> ValueError: invalid literal for int() with base 10: '2.'
>>>>>>>>>>
>>>>>>>>>> I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro
>>>>>>>>>> -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone
>>>>>>>>>>
>>>>>>>>>> were my input file is very simply
>>>>>>>>>>
>>>>>>>>>> Protein in water
>>>>>>>>>> 2410
>>>>>>>>>> 1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102
>>>>>>>>>> 1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978
>>>>>>>>>> 1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359
>>>>>>>>>> 1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621
>>>>>>>>>> 1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955
>>>>>>>>>> 1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275
>>>>>>>>>> 1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917
>>>>>>>>>> 1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378
>>>>>>>>>> 2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191
>>>>>>>>>> 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482
>>>>>>>>>> 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823
>>>>>>>>>> 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775
>>>>>>>>>> 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017
>>>>>>>>>> 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921
>>>>>>>>>> 2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469
>>>>>>>>>> 2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509
>>>>>>>>>> 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964
>>>>>>>>>> 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200
>>>>>>>>>> 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009
>>>>>>>>>> 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835
>>>>>>>>>> 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307
>>>>>>>>>> 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602
>>>>>>>>>> 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274
>>>>>>>>>> 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047
>>>>>>>>>> 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621
>>>>>>>>>> 2.91477 2.91477 2.91477
>>>>>>>>>>
>>>>>>>>>> Can you help me on that?
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> 2012/2/20 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>>>>>>>>>>> Hi Francesca,
>>>>>>>>>>>
>>>>>>>>>>> Is this the latest version
>>>>>>>>>>> (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)?
>>>>>>>>>>> If it is, please send me the input file and I'll fix the bug. Note
>>>>>>>>>>> that the previous version that was available online was one used in a
>>>>>>>>>>> workshop, while the script was still in beta.
>>>>>>>>>>>
>>>>>>>>>>> Cheers,
>>>>>>>>>>>
>>>>>>>>>>> Tsjerk
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini
>>>>>>>>>>> <francesca.vitalini11 at gmail.com> wrote:
>>>>>>>>>>>> Hi all,
>>>>>>>>>>>> I'm trying to coarsegrain my structure using the script martinize.py
>>>>>>>>>>>> and using my gro file as inmput and the dssp file with the second
>>>>>>>>>>>> structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the
>>>>>>>>>>>> pdb structure as input, I get the following error message that I
>>>>>>>>>>>> really don't understand.
>>>>>>>>>>>>
>>>>>>>>>>>> INFO Chain termini will be charged
>>>>>>>>>>>> INFO Residues at chain brakes will not be charged
>>>>>>>>>>>> INFO Local elastic bonds will be used for extended regions.
>>>>>>>>>>>> INFO Position restraints will be generated.
>>>>>>>>>>>> WARNING Position restraints are only enabled if -DPOSRES is set in
>>>>>>>>>>>> the MDP file
>>>>>>>>>>>> INFO Read input structure from file.
>>>>>>>>>>>> INFO Input structure is a GRO file. Chains will be labeled consecutively.
>>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>>> File "./martinize.py", line 2037, in <module>
>>>>>>>>>>>> for title,atoms,box in frameIterator(inStream):
>>>>>>>>>>>> File "./martinize.py", line 1303, in groFrameIterator
>>>>>>>>>>>> atoms = [groAtom(streamIterator.next()) for i in range(natoms)]
>>>>>>>>>>>> File "./martinize.py", line 1290, in groAtom
>>>>>>>>>>>> return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ",
>>>>>>>>>>>> 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44]))
>>>>>>>>>>>> ValueError: invalid literal for int() with base 10: '2.'
>>>>>>>>>>>>
>>>>>>>>>>>> Can anyone help me on that?
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Francesca
>>>>>>>>>>>> --
>>>>>>>>>>>> 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
>>>>>>>>>>> Molecular Dynamics Group
>>>>>>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>>>>>>>> * Zernike Institute for Advanced Materials
>>>>>>>>>>> University of Groningen
>>>>>>>>>>> The Netherlands
>>>>>>>>>>> --
>>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Francesca Vitalini
>>>>>>>>>>
>>>>>>>>>> PhD student at Computational Molecular Biology Group,
>>>>>>>>>> Department of Mathematics and Informatics, FU-Berlin
>>>>>>>>>> Arnimallee 6 14195 Berlin
>>>>>>>>>>
>>>>>>>>>> vitalini at zedat.fu-berlin.de
>>>>>>>>>> francesca.vitalini at fu-berlin.de
>>>>>>>>>>
>>>>>>>>>> +49 3083875776
>>>>>>>>>> +49 3083875412
>>>>>>>>>> --
>>>>>>>>>> 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
>>>>>>>>> Molecular Dynamics Group
>>>>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>>>>>> * Zernike Institute for Advanced Materials
>>>>>>>>> University of Groningen
>>>>>>>>> The Netherlands
>>>>>>>>> --
>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Francesca Vitalini
>>>>>>>>
>>>>>>>> PhD student at Computational Molecular Biology Group,
>>>>>>>> Department of Mathematics and Informatics, FU-Berlin
>>>>>>>> Arnimallee 6 14195 Berlin
>>>>>>>>
>>>>>>>> vitalini at zedat.fu-berlin.de
>>>>>>>> francesca.vitalini at fu-berlin.de
>>>>>>>>
>>>>>>>> +49 3083875776
>>>>>>>> +49 3083875412
>>>>>>>> --
>>>>>>>> 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
>>>>>>> Molecular Dynamics Group
>>>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>>>> * Zernike Institute for Advanced Materials
>>>>>>> University of Groningen
>>>>>>> The Netherlands
>>>>>>> --
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Francesca Vitalini
>>>>>>
>>>>>> PhD student at Computational Molecular Biology Group,
>>>>>> Department of Mathematics and Informatics, FU-Berlin
>>>>>> Arnimallee 6 14195 Berlin
>>>>>>
>>>>>> vitalini at zedat.fu-berlin.de
>>>>>> francesca.vitalini at fu-berlin.de
>>>>>>
>>>>>> +49 3083875776
>>>>>> +49 3083875412
>>>>>> --
>>>>>> 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
>>>>> Molecular Dynamics Group
>>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>>> * Zernike Institute for Advanced Materials
>>>>> University of Groningen
>>>>> The Netherlands
>>>>> --
>>>>> 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
>>>>
>>>>
>>>> --
>>>> Francesca Vitalini
>>>>
>>>> PhD student at Computational Molecular Biology Group,
>>>> Department of Mathematics and Informatics, FU-Berlin
>>>> Arnimallee 6 14195 Berlin
>>>>
>>>> vitalini at zedat.fu-berlin.de
>>>> francesca.vitalini at fu-berlin.de
>>>>
>>>> +49 3083875776
>>>> +49 3083875412
>>>
>>>
>>> --
>>> Francesca Vitalini
>>>
>>> PhD student at Computational Molecular Biology Group,
>>> Department of Mathematics and Informatics, FU-Berlin
>>> Arnimallee 6 14195 Berlin
>>>
>>> vitalini at zedat.fu-berlin.de
>>> francesca.vitalini at fu-berlin.de
>>>
>>> +49 3083875776
>>> +49 3083875412
>> --
>> Florian Dommert
>> Dipl. - Phys.
>>
>> Institute for Computational Physics
>> University Stuttgart
>>
>> Pfaffenwaldring 27
>> 70569 Stuttgart
>>
>> EMail: dommert at icp.uni-stuttgart.de
>> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>
>> Tel.: +49 - (0)711 - 68563613
>> Fax.: +49 - (0)711 - 68563658
>>
>> --
>> 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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>> 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. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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