[gmx-users] error while executing grompp

[Justin A. Lemkul]

Chanchal wrote:
> Hi Justin,
>   I am still getting the error message : Back Off! I just backed up 
> mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> processing topology...
> Generated 0 of the 595 non-bonded parameter combinations
> 
> -------------------------------------------------------
> Program grompp_d, VERSION 4.0.5
> Source code file: toppush.c, line: 1273
> 
> Fatal error:
> [ file topol.top, line 3879 ]:
> 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.
> -------------------------------------------------------
> 
> As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached 

The #define line is not present in that file.  Take care to use the right files 
when you've made changes.

-Justin

> is the file.
> Thanks
> Chanchal
> 
> 
> On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
>     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>
>         <mailto: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> <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 <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

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