[gmx-users] grompp segmentation error

ram bio rmbio861 at gmail.com
Thu Dec 31 15:24:28 CET 2009

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.


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