Hi Sara, That can only happen if the input file is empty. But I now see that the output file should be given as second argument, so it should be
./xtcrev.py input.xtc output.xtc rather than ./xtcrev.py input.xtc > output.xtc The latter will actually result in an empty xtc file. Maybe that's the cause of the problem? Sorry about that. Cheers, Tsjerk On Tue, Jan 10, 2012 at 6:38 PM, mohammad agha <mra...@yahoo.com> wrote: > Hi Tsjerk, > > I know that my question is silly but please help me. > I installed python2.5 on my system, then I ran "./xtcrev.py 1a.xtc > > 1a-rev.xtc" but it gave me following error: > > Traceback (most recent call last): > File "./xtcrev.py", line 54, in <module> > n = 92 + i(f.read(84)[-4:]) # Size of frame in bytes > File "./xtcrev.py", line 24, in i > > def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)]) > IndexError: string index out of range > > I know that j is out of range but I don't know that what should I do > exactly? > May I ask you to help me, Please? > > Best Regards > Sara > ________________________________ > From: Tsjerk Wassenaar <tsje...@gmail.com> > To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users > <gmx-users@gromacs.org> > Sent: Saturday, December 31, 2011 3:41 PM > > Subject: Re: Fw: [gmx-users] trjconv in martini > > Hi Sara, > >> # Extract the first part of the trajectory >> trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999 > > That should be -e 199999 :) But you can also use -e 200000. Probably > that is better. I first thought it'd be better to avoid a double > frame, but since trjcat is used to combine the parts again, it doesn't > matter. > > Good luck, > > Tsjerk > > > > -- > 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 -- 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
