Dear Amber Users,
I faced a problem when i ran MMPBSA with my own protein and ligand after 200ps MD simulation. I just want to try if my way to run MMPBSA is right or not, apparently my job didn't worked. This error message appeared when i ran MMPBSA.
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/farm/mirror/Programs/amber/amber11/bin/ptraj
mmpbsa_py_energy found! Using /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for GB calculations
mmpbsa_py_energy found! Using /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for PB calculations
Preparing trajectories for simulation...
20 frames were read in and processed by
ptraj for use in calculation.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
calculating receptor contribution...
Segmentation fault
Error: mmpbsa_py_energy error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
What's wrong with my job? what is the meaning of segmentation fault? here is my command to run MMPBSA:
nohup MMPBSA -O -i MMPBSA.in -o 6COX_s58k_MMPBSA.dat -sp 6COXAsolvoct.prmtop -cp 6COXSVak_netral.prmtop -rp 6COXSonly.prmtop -lp s58k.prmtop -y 6COXAsolvoct_md2_ntpr2.crd > MMPBSA.log &
Best Regards,
Muhammad Aditya Setiajid
University of Indonesia
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Received on Fri Apr 13 2012 - 01:30:05 PDT
