I tried to modify the spc.itp file, but wasn't successful. I decided not to try any more and changed to the amber_tip4p water model in the .top file. That solved the problem, no more error messages. Thanks for your help.
On Wed, Sep 16, 2009 at 7:30 PM, Gunnar Widtfeldt Reginsson < regins...@gmail.com> wrote: > I am trying to run grompp using a pdb file of DNA duplex, a sucessfully > generated topology, and the steep.mpd from > http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top > I am getting the fatal error: > > Fatal error: > [ file spc.itp, line 37 ]: > Atom index (1) in bonds out of bounds (1-0). > This probably means that you have inserted topology section "bonds" > in a part belonging to a different molecule than you intended to. > In that case move the "bonds" section to the right molecule. > > I am using the amber99 force field, and have followed the notes on nucleic > acids on http://chemistry.csulb.edu/ffamber/ > > I am new to Gromacs, can anyone help me with this? > > Thanks, > Gunnar W. >
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