[gmx-users] error while executing grompp

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 25 23:44:02 CEST 2009

Chanchal wrote:
> Hi All,
>    I have downloaded pdb file and required .top and .itp file from the 
> site http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I 
> execute the command
>  grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e 
> ener.edr -t traj.trr I got the error " Fatal error:
> [ file tip3p.itp, line 42 ]:
> Atom index (1) in settles out of bounds (1-0).
> This probably means that you have inserted topology section "settles"
> in a part belonging to a different molecule than you intended to.
> In that case move the "settles" section to the right molecule.
> -------------------------------------------------------
> Attached is the em.mdp file I am using. Please help me how to solve this 
> problem.

Please see here:


The .mdp file is not the source of the problem; the topology is.  If you need 
more help, you'll have to post the relevant section.


> Thanks
> Chanchal
> ------------------------------------------------------------------------
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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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