[gmx-users] error while executing grompp

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 26 02:10:56 CEST 2009



Chanchal wrote:
> Hi Justin,
>  I have corrected the ffcharmm.itp file. But I am still getting the 
> error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> 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.
> -------------------------------------------------------
> 

Well, then I'm out of ideas.  Your files work for me; I can successfully produce 
a .tpr file using a basic EM .mdp file.  Have you validated your installation 
using the test set?  Have you made any modifications to the standard tip3p.itp file?

-Justin

> Thanks
> Chanchal
> 
> 
> On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Chanchal wrote:
> 
>         Hi Justin,
>          Sorry, I attached the wrong file. Attached is the correct file.
> 
> 
>     There is a space after #define:
> 
>     #define _FF_CHARMM
> 
>     Your file has #define_FF_CHARMM.
> 
>     -Justin
> 
>         Thanks
>         Chanchal
> 
> 
> 
>         On Tue, Aug 25, 2009 at 4:56 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 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>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto: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>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto: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> <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> <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> <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

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