[gmx-users] error while executing grompp

Chanchal chanchal.kar at gmail.com
Wed Aug 26 01:02:15 CEST 2009


Hi Justin,
  Sorry, I attached the wrong file. Attached is the correct file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul <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>> 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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>>
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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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