[gmx-users] grompp segmentation error

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 31 19:19:22 CET 2009

ram bio wrote:
> Dear Gromacs Users,
> Iam following Drug/Enzyme complex solvation tutorial by John E.
> Kerrigan, I am unable to execute the grompp step as per the tutorial,
> the output of grompp command is as follows:
> grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr
>                                :-)  grompp  (-:
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Segmentation fault
> what i have done is as per the tutorial, that is
> 1) generated the drg.itp using prodrug beta
> 2) executed pdb2gmx using 4 that is ff53a6 ff
> 3) edit the drg.itp by removing the lines redundant as per trp.top
> 4) edit trp.gro by adding drg coordinates and chainging the numbers
> please help me to overcome this error, for your convenience I have
> attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files.

I doubt any of these files will be useful.  Better information would include:

1. The Gromacs version you are using.
2. The compilers used in installing Gromacs.
3. Options specified during configuration.
4. Specifications of your hardware.

A segmentation fault is a memory error and can have numerous causes.  The above 
information may be useful.


> Thanks,
> Ram
> 4 attachments —


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list