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