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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Apr 11, 2012, at 10:24 AM, "zhangaidi" <zhangaidi.mail.kiz.ac.cn> wrote: > > 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/ambero > utputs.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/ambero > utputs.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/ambero > utputs.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 > <files.rar> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Apr 11 2012 - 12:00:05 PDT