[gmx-users] error while executing grompp

Chanchal chanchal.kar at gmail.com
Tue Aug 25 23:24:42 CEST 2009

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
 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

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