[gmx-users] problems with martinize.py
francesca vitalini
francesca.vitalini11 at gmail.com
Mon Feb 20 16:05:48 CET 2012
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
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
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