[gmx-users] problems with martinize.py

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 20 14:01:27 CET 2012


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



More information about the gromacs.org_gmx-users mailing list