[gmx-users] error while executing grompp

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 25 23:49:38 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.

Your .mdp file isn't the problem. grompp is telling you what the problem 
is likely to be. The .top/.itp combination you are using is broken. See 


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