Dear Amber List,
We have recently install amber 11 and ambertools1.5 on our Linux cluster. The Calculation of the binding free energy of a protein-ligand complex was a success , but when I am running the MMPBSA decomposition calculation ,then I got error message during parse GB output files!(below). I don't know where is it going wrong. Any help would be appreciated. and I have attached the final results file as well as the run files.
The input file for mmpbsa:
Per-residue GB and PB decomposition
&general
endframe=50, verbose=1, interval=5,
/
&pb
istrng=0.100,
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=2, dec_verbose=3,print_res="71; 83; 204; 202; 475; 476"
/
Then I submit my job :
mpirun -np $NP MMPBSA.MPI -O -i mmpbsa_per_res_decomp.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp complex_solvated.prmtop -cp complex.prmtop -rp rp.prmtop -lp M6A.prmtop -y *.crd > progress.log 2>&1
The program stops after giving this error message:
Running MMPBSA.MPI on 6 processors...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home1/zhangad/zad/soft/amber11/bin/ptraj
sander found! Using /home1/zhangad/zad/soft/amber11/bin/sander for GB calculations
sander found! Using /home1/zhangad/zad/soft/amber11/bin/sander for PB calculations
Preparing trajectories for simulation...
10 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Error: Could not parse GB output files! Check for missing values (*********).
Error: Could not parse PB output files! Check for missing values (*********).
Traceback (most recent call last):
File "/home1/zhangad/zad/soft/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py.MPI", line 1489, in <module>
file3='_MMPBSA_ligand_pb.mdout', desc='\nPOISSON BOLTZMANN:\n\n')
File "/home1/zhangad/zad/soft/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 3284, in __init__
self.printdisper = not self.sander_apbs and not self._disperiszero()
File "/home1/zhangad/zad/soft/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 3720, in _disperiszero
abs(_avg(self.energy_data['edisper'][1])) > TOLERANCE or \
File "/home1/zhangad/zad/soft/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2122, in _avg
return sum(array) / len(array)
ZeroDivisionError: integer division or modulo by zero
I don't know where is it going wrong. Any help would be appreciated.
Cheers,
zhang aidi
dear
zhangaidi
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Received on Wed Apr 11 2012 - 07:30:08 PDT
