[gmx-users] Re: No molecules were defined in the system/ No such molecule type

sarah k dailycolors at gmail.com
Fri Sep 14 15:19:38 CEST 2012

> Dear Justin,

I reeditted my .top and .gro files for drug-complex simulation. Now after

"grompp -f em.mdp -c _b4ion.gro -p .top -o _b4ion.tpr" command, the
following messages appear and the procedure ends with no .tpr output:

Ignoring obsolete mdp entry 'title'

Ignoring obsolete mdp entry 'cpp'

 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#

checking input for internal consistency...

processing topology...

Opening library file /opt/bio/gromacs/share/gromacs/top/ffG43a1.itp

Opening library file /opt/bio/gromacs/share/gromacs/top/ffG43a1nb.itp

Opening library file /opt/bio/gromacs/share/gromacs/top/ffG43a1bon.itp

Opening library file /opt/bio/gromacs/share/gromacs/top/ff_dum.itp

Segmentation fault

I checked my _b4ion.gro and the SOL added .top file. The formattings seemed
normal to me. ff_dum.itp file also had no problem. What can be the reason?

p.s. I've simulated the protein successfully with GROMOS96 forcefield on
Gromacs 4.0.5 and need to compare that with the complex results so I'm just
using the .mdp files and all the parameters applied in the free protein

Thanks for your previous responce,


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