[gmx-users] error while executing grompp
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 26 00:42:40 CEST 2009
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>> 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> | (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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