Hi, Did you get my script ? I dump a frame from .trr file. I did not define xtc-grps
On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> I got an error when do grompp: The input PDB file comes from the output >> of GROMACS by trajconv command. >> >> > <snip> > > ------------------------------------------------------- >> Program grompp, VERSION 3.3.3 >> Source code file: ../../../../src/kernel/readir.c, line: 838 >> >> *Fatal error: >> Invalid atom number 6415 in indexfile* >> ------------------------------------------------------- >> >> > Instead of screen dumps, it would be a lot more useful to see your .mdp > file, as well as the command line (not output from) both grompp and trjconv. > Did you dump the frame from an .xtc file? What did you specify in > xtc-grps? > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [email protected] ([email protected] or [email protected]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
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