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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