[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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