[gmx-users] Another problem with DNA

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 17 15:18:27 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?

By default, SPC is not intended for use with the AMBER force fields.  You will 
have to modify the spc.itp file to be compatible with AMBER:


If grompp cannot satisfy any of the existing #ifdef statements in the [atoms] 
directive, it believes that there are no water atoms, hence raising the error 
when it attempts to process bonds on line 37 of spc.itp.


> Thanks,
> Gunnar W.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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