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-- Thank you, With regards, B. Sangeetha Ph.D Scholar, Centre for Bioinformatics, Pondicherry University, Pondicherry, India On Wed, Feb 8, 2012 at 1:35 AM, Jason Swails <jason.swails.gmail.com> wrote: > I found the bug. I didn't catch it at first because it had already been > fixed in the development version. I created a bugfix for it (on > http://ambermd.org/bugfixesat.html) which should appear sometime in the > next day or two. I verified after applying that fix that it properly > parsed your files. It will be bugfix.27 on that page. > > Thanks for the report! > Jason > > On Tue, Feb 7, 2012 at 11:51 AM, Jason Swails <jason.swails.gmail.com > >wrote: > > > I can't see anything wrong with your nm output files. Does the MMPBSA.py > > test pass for normal mode entropy calculations? > > > > On Tue, Feb 7, 2012 at 6:52 AM, Sangeetha B <sangeetha.bicpu.edu.in > >wrote: > > > >> Hi, > >> > >> I am still expecting some solutions for my problem in running Normal > mode > >> analysis. > >> > >> > >> > >> -- > >> 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 > >> > > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > >> > > > > > > -- > > Jason M. Swails > > > > Quantum Theory Project, > > University of Florida > > Ph.D. Candidate > > 352-392-4032 > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Candidate > 352-392-4032 > _______________________________________________ > 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 Feb 08 2012 - 07:00:02 PST