[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
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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
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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
>>> --
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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
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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
> --
> 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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