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-- Thank you, With regards, B. Sangeetha Ph.D Scholar, Centre for Bioinformatics, Pondicherry University, Pondicherry, India ---------- Forwarded message ---------- From: Sangeetha B <sangeetha.bicpu.edu.in> Date: Thu, Feb 2, 2012 at 9:48 AM Subject: Re: [AMBER] NMODE list index out of range error To: AMBER Mailing List <amber.ambermd.org> Hi, Thanks for the reply.. After the minimization of each frame, it says "convergence satisfied". I have attached all the _MMPBSA_*_nm.out files as a zipped archive with this mail. I thank you a lot in advance. It will be very helpful if someone can solve this issue.. -- Thank you, With regards, B. Sangeetha Ph.D Scholar, Centre for Bioinformatics, Pondicherry University, Pondicherry, India On Sat, Jan 28, 2012 at 9:12 PM, Jason Swails <jason.swails.gmail.com>wrote: > Can you send your _MMPBSA_*_nm.out files so I can take a look at them? > > It appears that for some reason one of the snapshots didn't minimize > completely and so there are different numbers of frames for the complex > receptor and ligand. However, MMPBSA should have exited more gracefully or > readjusted silently. > > It may also be the case that no snapshot could minimize enough for the > complex or receptor or something, so there was no data to analyze. Again, > the error reporting should be better. > > All the best, > Jason > > -- > 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/amber >