[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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