[gmx-users] problems with martinize.py
francesca vitalini
francesca.vitalini11 at gmail.com
Mon Feb 20 13:57:16 CET 2012
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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