[gmx-users] Another problem with DNA

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 17 15:25:26 CEST 2009

Gunnar Widtfeldt Reginsson 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?

Their website example .top uses amber_tip4p water, while their website 
pdb2gmx instructions won't replicate this. Please take that up with them.

Your inclusion of spc.itp is probably in the wrong place. You need all [ 
moleculetypes ] before [ system ] and [ molecules ] and all parts of a [ 
moleculetype ] need to follow each other directly. See example in 
chapter 5 of the manual.


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