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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