[gmx-users] problems with martinize.py
Tsjerk Wassenaar
tsjerkw at gmail.com
Mon Feb 20 14:29:59 CET 2012
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
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>>>>
>>>>
>>>>
>>>> --
>>>> 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
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>>>
>>>
>>>
>>> --
>>> 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
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>>
>>
>>
>> --
>> 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
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