[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:

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?

Gunnar W.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090916/35aaca14/attachment.html>

More information about the gromacs.org_gmx-users mailing list