[AMBER] segmentation fault when using mmpbsa.py

From: Chris Chris <alpharecept.yahoo.com>
Date: Wed, 30 Mar 2011 15:03:46 -0700 (PDT)

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
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