[gmx-users] grompp segmentation error

[Justin A. Lemkul]

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.

-Justin

> Thanks,
> 
> Ram
> 4 attachments —

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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