Hi All,<br> I have downloaded pdb file and required .top and .itp file from the site <a href="http://www.bioinf.uni-sb.de/RB/">http://www.bioinf.uni-sb.de/RB/</a> for DOPC simulation. Now when I execute the command <br> 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:<br>
[ file tip3p.itp, line 42 ]:<br>Atom index (1) in settles out of bounds (1-0).<br>This probably means that you have inserted topology section "settles"<br>in a part belonging to a different molecule than you intended to.<br>
In that case move the "settles" section to the right molecule.<br>-------------------------------------------------------<br><br>Attached is the em.mdp file I am using. Please help me how to solve this problem.<br>
<br>Thanks<br>Chanchal<br><br>