[gmx-users] error while executing grompp
Chanchal
chanchal.kar at gmail.com
Wed Aug 26 01:14:23 CEST 2009
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.
-------------------------------------------------------
Thanks
Chanchal
On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul <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>> 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>>> 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>>>> 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> | (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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>> gmx-users mailing list gmx-users at gromacs.org
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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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>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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