I am performing mmpbsa analysis using mmpbsa.py. I combined three different
trajectories into one using ptraj via the following:
trajin g1octa_prod_mdx1
trajin g1octa_prod_mdx2
trajin g1octa_prod_mdx3
trajout g1octa_combined_mdx
the mmpbsa submit file is as follows:
#!/bin/csh
#
#PBS -l walltime=48:00:00
#PBS -l mem=100gb
#PBS -l ncpus=16
#PBS -q normal
#PBS -V
#PBS -N mmpbsa_g1octa
#PBS -o mmpbsa_g1octa.out
#PBS -e mmpbsa_g1octa.err
#------------------------------
# End of embedded QSUB options
# echo commands before execution; use for debugging
# remove # from the line below to use
set echo
set JOBID=`echo $PBS_JOBID | cut -d'.' -f1`
cd $SCR
saveafterjob "tar cf ${PBS_JOBNAME}.${JOBID}.tar *"
cp /u/ac/cgaughan/mmpbsa_g1octa.in $SCR
cp /u/ac/cgaughan/g1octa.top $SCR
cp /u/ac/cgaughan/g1octa_nosolv.top $SCR
cp /u/ac/cgaughan/g1hexa_4octa_nosolv.top $SCR
cp /u/ac/cgaughan/g1dimer_4octa_nosolv.top $SCR
cp /u/ac/cgaughan/g1octa_combined_mdx $SCR
mpirun -np 16 /gpfs1/apps/chemistry/amber/amber11/bin/MMPBSA.py -O -i
mmpbsa_g1octa.in -o G1OCTA_RESULTS_MMPBSA.dat -sp g1octa.top -cp
g1octa_nosolv.top -rp g1hexa_4octa_nosolv.top -lp g1dimer_4octa_nosolv.top -y
g1octa_combined_mdx
The job is run in the scratch directory with the files compressed and sent
directly to mass storage when the job is done.
It seemed as though the job would be completed, however I recieved a
segmentation error as can be seen in the attached .err file. I also attached the
.out file as well.
It appears that the main problem was:
Could not predict number of frames for AMBER trajectory file
It appears as though a final report was being printed at the end of the job but
there is no data in it:
|Input file:
|--------------------------------------------------------------
|
|&general
|startframe=6000, endframe=8000, interval=1,
|verbose=2, keep_files=0, receptor_mask=:1-112:223-334,
ligand_mask=:113-140:335-362,
|/
|&gb
|igb=2,
|/
|&pb
|fillratio=4.0,
|/
|
|--------------------------------------------------------------
|Solvated complex topology file: g1octa.top
|Complex topology file: g1octa_nosolv.top
|Receptor topology file: g1hexa_4octa_nosolv.top
|Ligand topology file: g1dimer_4octa_nosolv.top
|Initial mdcrd(s): g1octa_combined_mdx
|Calculations performed using 2001 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Can someone help me make sense of all this? As can be seen in the .out file, the
job ran for ~ 7 hours. What would cause it to crash towards the end of the job?
Thanks for any help,
Chris
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Received on Wed Mar 30 2011 - 15:30:03 PDT
