[AMBER] Error: Could not parse GB output files! Check for missing values (*********).

From: zhangaidi <zhangaidi.mail.kiz.ac.cn>
Date: Wed, 11 Apr 2012 22:24:50 +0800





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
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