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:
http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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