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.vitalin...@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 <tsje...@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.vitalin...@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 <tsje...@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.vitalin...@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@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-requ...@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@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-requ...@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 >>> >>> vital...@zedat.fu-berlin.de >>> francesca.vital...@fu-berlin.de >>> >>> +49 3083875776 >>> +49 3083875412 >>> -- >>> gmx-users mailing list gmx-users@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-requ...@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@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-requ...@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 > > vital...@zedat.fu-berlin.de > francesca.vital...@fu-berlin.de > > +49 3083875776 > +49 3083875412 > -- > gmx-users mailing list gmx-users@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-requ...@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
