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
