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-- Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine. > From: "Ray Luo, Ph.D." <ray.luo.uci.edu> > Date: Mon, 1 Aug 2011 17:48:04 -0700 > To: Roman Osman <roman.osman.mssm.edu> > > Rami, > > MJ is running your job, it's slow ... but the patched code seems to be > working on Mac ... MJ is running it on Linux right now ... ---- MMPBSA -O -i decomp_lig.in -o decomp_lig.dat -sp ./cbp_ro 5_200_py.top -cp ./cbp_ro5_nw_py.top -rp ./cbp_3dwy_py.top -lp ./ro5_py.top -y . /cbp_ro5_200.trj -do cbp_ror3_decnw.dat Reading command-line arguments and input files... Loading and checking parameter files for compatibility... ptraj found! Using /home/mjhsieh/amber11/bin/ptraj sander found! Using /home/mjhsieh/amber11/bin/sander for GB calculations sander found! Using /home/mjhsieh/amber11/bin/sander for PB calculations nmode program found! Using /home/mjhsieh/amber11/bin/mmpbsa_py_nabnmode Preparing trajectories for simulation...100 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... Beginning nmode calculations with mmpbsa_py_nabnmode... Calculating normal modes for 3 frames calculating complex contribution for frame 0 calculating receptor contribution for frame 0 calculating ligand contribution for frame 0 calculating complex contribution for frame 1 calculating receptor contribution for frame 1 calculating ligand contribution for frame 1 calculating complex contribution for frame 2 calculating receptor contribution for frame 2 calculating ligand contribution for frame 2 Traceback (most recent call last): File "/home/mjhsieh/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py", line 1343, in <module> outfile.write(str(nmodenorm)) File "MMPBSA_mods/amberoutputs.py", line 2263, in __str__ File "MMPBSA_mods/amberoutputs.py", line 2302, in AvgStdev File "MMPBSA_mods/amberoutputs.py", line 2319, in _tot_stdevs IndexError: list index out of range _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Aug 02 2011 - 09:30:02 PDT