Custom Search
-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jan 28, 2012, at 1:43 AM, Sangeetha B <sangeetha.bicpu.edu.in> wrote: > Hi, > > I have done a 5ns simulation for a protein-ligand complex and I want to > calculate the entropy of binding for this complex using Normal Mode > analysis. > I have restricted my calculation to include only the residues within 12 > angstroms of the active site. > I run this nmode in serial in CPU mode of Tesla C2050 with a 16 GB RAM. > When i run this even for something as less as 2 frames, i get the following > error. > > Reading command-line arguments and input files... > Loading and checking parameter files for compatibility... > ptraj found! Using /usr/local/amber11/bin/ptraj > nmode program found! Using /usr/local/amber11/bin/mmpbsa_py_nabnmode > Preparing trajectories for simulation... > 500 frames were read in and processed by ptraj for use in calculation. > > > Beginning nmode calculations with mmpbsa_py_nabnmode... > Calculating normal modes for 2 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 > Traceback (most recent call last): > File "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py", line 1344, > in <m > odule> > outfile.write(str(nmodenorm)) > File > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py" > , line 2263, in __str__ > totavg, totstdev = self.AvgStdev() > File > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py" > , line 2302, in AvgStdev > stdev = self._tot_stdevs() > File > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py" > , line 2319, in _tot_stdevs > sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i] > IndexError: list index out of range > > > The input file that I used is as below: > > Input file: > |-------------------------------------------------------------- > |NMODE > |&general > | verbose=1, interval=5, strip_mdcrd=0, > |/ > |&nmode > | maxcyc=50000, nminterval=250, nmode_igb=1, > |/ > > and the command I used to run this is "/usr/local/amber11/bin/MMPBSA -i > nm_5e.in -cp comp_strip.prmtop -rp prot_strip.prmtop -lp > ligand5e_vac.prmtop -y comp5e_md1_5_12a.mdcrd" > > A file named "FINAL_RESULTS_MMPBSA.dat" is being generated but there is no > Delta S value in it.. The contents of this file is shown below: > > | Run on Fri Jan 27 23:13:57 IST 2012 > > |Input file: > |-------------------------------------------------------------- > |NMODE > |&general > | verbose=1, interval=5, strip_mdcrd=0, > |/ > |&nmode > | maxcyc=50000, nminterval=250, nmode_igb=1, > |/ > |-------------------------------------------------------------- > |Complex topology file: comp_strip.prmtop > |Receptor topology file: prot_strip.prmtop > |Ligand topology file: ligand5e_vac.prmtop > |Initial mdcrd(s): comp5e_md1_5_12a.mdcrd > | > |Best guess for receptor mask: ":1-109" > |Best guess for ligand mask: ":110" > |Ligand residue name is "UNK" > | > |Calculations performed using 500 frames. > |NMODE calculations performed using 2 frames. > | > |All units are reported in kcal/mole. > |All entropy results have units kcal/mole (Temperature is 298.15 K). > ------------------------------------------------------------------------------- > ------------------------------------------------------------------------------- > > > Can someone please tell me what is going wrong... Is the problem with the > memory available in the system? > _______________________________________________ > 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 Sat Jan 28 2012 - 08:00:03 PST