[gmx-users] Another problem with DNA
Gunnar Widtfeldt Reginsson
reginsson at gmail.com
Wed Sep 16 20:30:58 CEST 2009
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully
generated topology, and the steep.mpd from
I am getting the 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?
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