Hi Fabricio, You can also sue the option -dump 10000 to extract a frame. But it's not related to your error. Have you done any fitting and pbc related stuff or did you shuffle/sort your system prior to running?
Cheers, Tsjerk On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <[EMAIL PROTECTED]> wrote: > Hello, > I have ran a simulation with gromac but can't seem to be able to extract a > single structure of a determined frame from my .trr file. I wish to obtain a > pdb file good for reading in CHIMERA, for example. > I tryed the following command: > trjconv -f sim.trr -s trjtop.tpr -o pdbiwant.pdb -b 10000 -e 10000. > Some programs, spdbv, for example, completely mess up my structure, making > bonds where it shouldn't etc etc. CHIMERA simply cannot find any coordinates > in the file. But the .pdb generated from trjconv looks ok. I mean , there > are coordinates and all. > Any suggestions? > Thank you in advance > FabrÃcio Bracht > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
