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

[Justin Lemkul]

On 9/14/12 9:19 AM, sarah k wrote:
>>
>> 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
>
>

Unfortunately this type of error doesn't really provide any helpful information 
as to what's wrong.  A segmentation fault is a generic memory error (see Google 
for more thorough discussions).  The main reasons why grompp might seg fault:

1. Files are unavailable
2. Files are misformatted
3. Libraries have moved

-Justin

>
> 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
> simulation.
>
> Thanks for your previous responce,
>
> Sarah
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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