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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