I am running a binding energy calculation (MM-PBSA) for protein-ligand complex using Amber11 and AmberTools 1.5. I am following a Ross Walker tutorial (Link: http://ambermd.org/tutorials/advanced/tutorial3/), but have got error message during MMPBSA calculation as follows:
saugata@saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/saugata/amber11/bin/ptraj
mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy for GB calculations
mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy for PB calculations
Preparing trajectories for simulation...
50 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
calculating receptor contribution...
Segmentation fault (core dumped)
Error: mmpbsa_py_energy error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
saugata@saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA.py --clean
MMPBSA.py: command not found
saugata@saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA --clean
Reading command-line arguments and input files...
Cleaning temporary files
saugata@saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
Does anyone have any suggestions?
Thank you in advance.
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