[gmx-users] problems with martinize.py
francesca vitalini
francesca.vitalini11 at gmail.com
Mon Feb 20 16:51:44 CET 2012
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
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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> 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
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