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
