Hi Sara, If you give two arguments, it shouldn't do that. './xtcrev.py input.xtc output.xtc' should work fine. Of course I could've clogged the script with checking the number of input files and such, and maybe I will later, but for now it's just a nifty hack :p
Cheers, Tsjerk On Wed, Jan 11, 2012 at 11:05 AM, mohammad agha <mra...@yahoo.com> wrote: > Hi Tsjerk, > > Thank you very much from your reply. Yes, you're right, I corrected that, > but now it gave me this error: > > Traceback (most recent call last): > File "./xtcrev.py", line 68, in <module> > o = open(sys.argv[2],"w") > IndexError: list index out of range > > 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: Wednesday, January 11, 2012 12:54 PM > > Subject: Re: Fw: [gmx-users] trjconv in martini > > 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 -- 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
