[gmx-users] error while executing grompp

[Justin A. Lemkul]

Your ffcharmm.itp file lacks a necessary line at the very top:

#define _FF_CHARMM

Without this line, grompp does not know which force field you are using, and 
hence everything breaks down when other .itp files are called.

-Justin

Chanchal wrote:
> Hi,
>   Attached are the top and itp file I am using. Please help me to fix 
> the problem.
> Thanks
> Chanchal
> 
> 
> On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

========================================